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Variant interpretation report

HFE c.193A>T, p.Ser65Cys

NM_000410.4:c.193A>T NP_000401.1:p.(Ser65Cys) Missense · exon 2 View identifiers
Classification
Uncertain significance

Variant description:

The HFE NM_000410.4:c.193A>T (NP_000401.1:p.(Ser65Cys)) missense variant has not previously been reported in somatic cancers (COSMIC). Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About HFE

HFE encodes a cell-surface protein that helps regulate the body’s iron absorption by influencing how transferrin interacts with its receptor. Inherited changes in HFE can cause hereditary hemochromatosis, a disorder in which the body stores too much iron. HFE can also be altered in cancer, and inherited HFE changes may increase the risk of some cancers.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 0
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

VUS: no adjudicated criteria are applied, so no generic ACMG/AMP 2015 pathogenic, likely pathogenic, benign, or likely benign combination is met.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
22,016 / 1,614,088 alleles

gnomAD v4.1: 22,016 / 1,614,088 alleles. Recorded AF 0.0136399. Recorded homozygote count 195.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.01022; MAF= 1.02200%, 2891/282878 alleles, homozygotes = 24) and has highest observed frequency in the European (Finnish) population (AF= 0.0213774; MAF= 2.13774%, 537/25120 alleles, homozygotes = 9); grpmax FAF= 0.0149203.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

No screenshot for this evidence
REVEL score
0.549 recorded score

Recorded REVEL score: 0.549. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied
ClinVar submissions
16 reported laboratory submissions

9 Uncertain significance · 4 Likely benign · 2 Benign · 1 Uncertain Significance. ClinVar API review status: criteria provided, conflicting classifications.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. HFE, a transmembrane protein, is altered by mutation in various cancers. Germline HFE mutations are associated with hemochromatosis and predispose to

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.

28 criteria with recorded statuses: 0 met · 13 not met · 11 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

PS4 is not met because the exact-variant case-control data yield OR 1.50 with 95% CI 0.62–3.64, failing the required OR >5.0 and CI-not-including-1.0 thresholds.

PP4 and BP5 remain not assessed because case-level phenotype/family-history and alternate-molecular-basis information are unavailable.

PP5 and BP6 are not met because ClinVar has zero exact-variant expert-panel submissions and ordinary laboratory or literature-only assertions are excluded.

The variant is missense, so PP3 and BP4 are adjudicated exclusively through the REVEL path under the generic rules.

REVEL 0.549 is below the PP3 supporting cutoff and above the BP4 supporting cutoff; neither computational criterion is met.

Not met · 13 · evaluated, threshold not reached

PS1 ACMG_2015Not met: no different-nucleotide HFE variant producing p.Ser65Cys is established as pathogenic in the reviewed evidence. Details ▾Hide ▴
Reasoning

The variant is HFE p.Ser65Cys (c.193A>T). The reviewed evidence documents this exact amino-acid substitution and reports it as a common polymorphism/risk factor with mild or variable iron-overload associations, but does not identify a different nucleotide change producing p.Ser65Cys that has been established as pathogenic. Therefore the required same-amino-acid pathogenic comparator for PS1 is absent.

Rule
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Evidence considered
  • ClinVar identifies the exact variant as NM_000410.4(HFE):c.193A>T (p.Ser65Cys); the reviewed record provides no established pathogenic alternate nucleotide change for the same amino-acid substitution.
  • The HFE review describes S65C as a risk factor rather than a causative mutation and reports a frequency of 1.6–5.5% on Caucasian chromosomes.
  • The population/clinical study found S65C in 8 of 250 healthy controls, with a 1.6% allele frequency, and in 14 of 296 patients evaluated for suspected iron overload.
Sources
PS4 ACMG_2015Not met: HFE S65C had OR 1.50 (95% CI 0.62–3.64), below the >5.0 threshold and with a confidence interval including 1.0. Details ▾Hide ▴
Reasoning

Generic ACMG/AMP PS4 requires a significantly increased prevalence in affected individuals, with RR or OR >5.0 and a confidence interval that does not include 1.0. Holmström et al. (PMID:12377814) reported the exact HFE S65C variant in 14/296 patients evaluated for suspected iron overload and 8/250 healthy controls. Treating these as carrier counts, I computed the case-control odds ratio as (14×242)/(282×8)=1.50 with an approximate 95% CI of 0.62–3.64. The OR is not >5.0 and the CI includes 1.0, so PS4 is not met. The paper also reported allele-frequency enrichment in non-C282Y/non-H63D patient chromosomes (4.9% versus 1.9% in controls, p<0.05), but that result does not satisfy the specified PS4 OR and confidence-interval thresholds.

Rule
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
Evidence considered
  • Holmström et al. 2002, abstract/Results and Tables 2, 4, 5, and 7: HFE S65C was found in 14 patients and 8 controls; patient cohort 296 and healthy-control cohort 250.
  • Computed case-control OR from carrier counts: (14/282)/(8/242) = 1.50; approximate 95% CI 0.62–3.64.
  • The same paper reports S65C allele frequency enrichment in non-C282Y/non-H63D patient chromosomes versus controls, 4.9% versus 1.9%, p<0.05, but the specified PS4 OR and CI thresholds are not met.
Sources
PM1 ACMG_2015Not met: gnomAD v4.1 reports AF 0.0136399, and no validated HFE hotspot or benign-variation-free critical domain is established. Details ▾Hide ▴
Reasoning

HFE p.Ser65Cys lies within an annotated MHC class I-like antigen-recognition region, but the generic PM1 requirement is a mutational hotspot or critical, well-established functional domain without benign variation. No validated HFE hotspot or critical-domain specification is present, the hotspot search was negative, and p.Ser65Cys itself is frequent in population controls (gnomAD v4.1 AF 0.0136399; gnomAD v2.1 AF 0.01022), providing benign variation at the relevant site. The available review also reports no evident effect on HFE protein structure.

Rule
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
Evidence considered
  • The variant annotation places p.Ser65Cys in the MHC class I-like antigen recognition-like domain (IPR011161), but this annotation does not establish that the region is a critical functional domain for generic PM1.
  • gnomAD v4.1 reports p.Ser65Cys at AF 0.0136399 (22,016/1,614,088 alleles; 195 homozygotes), and gnomAD v2.1 reports AF 0.01022 (2,891/282,878 alleles; 24 homozygotes).
  • The Cancer Hotspots search found no statistically significant hotspot for HFE S65.
  • The HFE review states that S65C produces no evident effect on HFE protein structure and should be considered a risk factor rather than a causative mutation.
  • The clinical/population study found S65C in eight healthy controls at a 1.6% allele frequency.
Sources
PM2 ACMGNot met: gnomAD v4.1 AF is 1.36%, far above the 0.01% PM2 threshold, with 195 homozygotes observed. Details ▾Hide ▴
Reasoning

Generic PM2 requires absence from controls or an extremely low frequency. The default all-comers population sources are applicable because no governing VCEP specifies a non-cancer or exome-only source. The variant is common in gnomAD v2.1 (AF 0.01021995; grpmax FAF 0.0149203) and gnomAD v4.1 (AF 0.0136399; grpmax FAF 0.0160786), far above the generic PM2 supporting threshold of 0.0001. The gnomAD v2.1 non-cancer exome subset is also positive at AF 0.00999781, so restricting to that subset would not change the conclusion.

Rule
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
Evidence considered
  • gnomAD v2.1 all-comers: AF=0.01021995, 2,891/282,878 alleles, 24 homozygotes, grpmax FAF=0.0149203.
  • gnomAD v4.1 all-comers: AF=0.0136399, 22,016/1,614,088 alleles, 195 homozygotes, grpmax FAF=0.0160786.
  • The available gnomAD v2.1 non-cancer exome subset is also positive: AF=0.00999781, 2,369/236,952 alleles, 21 homozygotes, grpmax FAF=0.0146884.
  • The generic PM2 calibration supplied for this case is <=0.0001; all available population frequencies are orders of magnitude higher.
Sources
PM5 ACMG_2015Not met: no different missense substitution at HFE residue 65 is established as pathogenic in the reviewed comparator evidence. Details ▾Hide ▴
Reasoning

The target is HFE p.Ser65Cys. The reviewed same-residue comparator search contains no candidate alternate missense variant at residue 65 with an established pathogenic classification. The available HFE literature discusses S65C itself and other HFE residues, not a pathogenic different missense substitution at Ser65. Therefore PM5 is not met.

Rule
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Evidence considered
  • The same-residue comparator artifact contains zero candidates and zero confirmed pathogenic alternate missense variants at residue 65.
  • The HFE review identifies S65C as the Ser65 substitution and characterizes it as a risk factor rather than a causative mutation; it does not report a pathogenic alternate missense change at Ser65.
  • The clinical/population study reports observations for S65C and does not establish a different pathogenic missense substitution at residue 65.
Sources
PP2 ACMG_2015Not met: HFE p.Ser65Cys has gnomAD v4.1 AF 0.0136399, inconsistent with a low rate of benign missense variation. Details ▾Hide ▴
Reasoning

PP2 requires both a low rate of benign missense variation and missense variants as a common disease mechanism. HFE has substantial benign/common missense variation: p.Ser65Cys has gnomAD v4.1 AF 0.0136399 and gnomAD v2.1 AF 0.01022, and the literature reports S65C at 1.6–5.5% on Caucasian chromosomes. Although HFE disease-associated alleles include missense variants, the low-benign-missense-variation requirement is not satisfied.

Rule
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Evidence considered
  • gnomAD v4.1 reports p.Ser65Cys AF 0.0136399, including 195 homozygotes; gnomAD v2.1 reports AF 0.01022, including 24 homozygotes.
  • The HFE review reports S65C frequency of 1.6–5.5% on Caucasian chromosomes and describes it as a risk factor rather than a causative mutation.
  • The clinical/population study found S65C in eight healthy controls with a 1.6% allele frequency.
Sources
PP3 ACMGNot met: missense-path REVEL score 0.549 is below the PP3 supporting threshold of 0.644. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, so the governing generic path is REVEL only; SpliceAI and BayesDel are not used for PP3 in this situation. REVEL is 0.549, below the generic PP3 supporting threshold of >= 0.644 (ClinGen SVI REVEL calibration, PMID:36413997), so PP3 is not met.

Rule
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Evidence considered
  • Variant consequence: missense, NP_000401.1:p.(Ser65Cys); therefore the generic missense path uses REVEL only.
  • Local REVEL lookup reports score 0.549 for NM_000410.4:c.193A>T.
  • The supplied ClinGen SVI REVEL calibration sets PP3 supporting at >= 0.644; this threshold is attributed to Pejaver et al. 2022, PMID:36413997.
  • SpliceAI max delta 0.028 and BayesDel 0.105529 were not counted because they are not the governing predictor path for a missense PP3 assessment; BayesDel has no established generic ACMG-strength calibration.
Sources
revel
PP5 ACMG_2015Not met: ClinVar reports zero exact-variant expert-panel submissions, so no qualifying Pathogenic or Likely pathogenic source supports PP5. Details ▾Hide ▴
Reasoning

Generic ACMG/AMP PP5 requires a reputable source to report the variant as pathogenic when the evidence is not available to the laboratory for independent evaluation. ClinVar has no exact-variant expert-panel classification for HFE NM_000410.4:c.193A>T (p.Ser65Cys); expert-panel submissions are zero, and the available Pathogenic entry is an OMIM literature-only submission without assertion criteria. Ordinary laboratory submissions, conflicting aggregate labels, and non-expert assertions do not qualify under the requested PP5 rule.

Rule
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
  • ClinVar exact-variant record NM_000410.4(HFE):c.193A>T (p.Ser65Cys), variation ID 11: expert-panel submissions = 0; overall classification is conflicting.
  • The exact-variant Pathogenic OMIM submission is literature-only and has no assertion criteria; it is not an expert-panel classification and is excluded from PP5.
  • The exact-variant Likely benign and Benign entries are single-submitter clinical laboratory assertions and are not qualifying expert-panel evidence for PP5.
Sources
BA1 ACMGNot met: gnomAD v4.1 grpmax FAF is 1.61%, below the 5% BA1 threshold, and the 2.64% Amish popmax is based on only 910 alleles. Details ▾Hide ▴
Reasoning

Generic BA1 requires a filtering allele frequency of at least 0.05. The appropriate grpmax FAF is 0.0149203 in gnomAD v2.1 and 0.0160786 in gnomAD v4.1, both below 0.05. The Amish v4.1 popmax point estimate of 0.0263736 is based on only 24/910 alleles, below the required 2000 observed alleles for using a population frequency estimate, and is not the filtering FAF. The variant is also described in the literature as a risk factor rather than a causative HFE mutation, but the frequency does not reach the stand-alone threshold regardless.

Rule
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
Evidence considered
  • gnomAD v2.1: total AF 0.01021995 from 2,891/282,878 alleles; grpmax FAF=0.0149203; highest point estimate was Finnish AF 0.0213774 from 537/25,120 alleles.
  • gnomAD v4.1: total AF 0.0136399 from 22,016/1,614,088 alleles; grpmax FAF=0.0160786; highest point estimate was Amish AF 0.0263736 from 24/910 alleles, below the 2000-observed-allele requirement.
  • The molecular genetics of haemochromatosis (PMID:16132052) reports S65C at 1.6–5.5% on Caucasian chromosomes and describes it as a risk factor rather than a causative mutation.
Sources
BS2 ACMG_2015Not met: 195 gnomAD v4.1 homozygotes are observed, but HFE disease is late-onset/reduced-penetrance and healthy adult status with early full penetrance is not established. Details ▾Hide ▴
Reasoning

The variant is observed in homozygotes in population data (24 in gnomAD v2.1 and 195 in gnomAD v4.1), but this does not establish healthy adult homozygotes with full penetrance expected at an early age. HFE-related hemochromatosis is late-onset and reduced-penetrance, and the available S65C study does not provide a qualifying healthy-adult homozygote observation. Therefore the ACMG/AMP BS2 evidence requirement is not met.

Rule
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Evidence considered
  • gnomAD v2.1 reports 24 homozygotes and gnomAD v4.1 reports 195 homozygotes; these population records do not establish that the individuals were healthy adults evaluated for an early-onset fully penetrant disorder.
  • Mild iron overload in patients carrying the HFE S65C gene mutation (PMID:12377814) studied 250 healthy controls and reported S65C in 8 controls at 1.6% allele frequency, but did not provide a qualifying healthy-adult S65C homozygote observation; one examined S65C homozygous relative had iron deficiency.
  • The molecular genetics of haemochromatosis (PMID:16132052) characterizes S65C as a risk factor rather than a causative mutation, inconsistent with the full-penetrance early-onset assumption required for BS2.
Sources
BP1 ACMG_2015Not met: HFE hereditary hemochromatosis is chiefly associated with recurrent missense alleles C282Y and H63D, not primarily truncating variants. Details ▾Hide ▴
Reasoning

BP1 applies when primarily truncating variants are known to cause disease. The HFE disease literature instead identifies recurrent missense alleles, especially C282Y and H63D, as the principal hereditary hemochromatosis variants and discusses S65C as a missense risk allele. Thus the available evidence does not support a primarily truncating disease mechanism for HFE.

Rule
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Evidence considered
  • The HFE review states that most affected individuals carry the C282Y missense mutation, describes H63D as a milder missense allele, and discusses S65C as another missense risk allele.
  • The study of 711 hemochromatosis probands describes C282Y and H63D as the established HFE missense mutations and evaluates S65C as a further missense variant; it does not establish a primarily truncating HFE disease mechanism.
Sources
BP4 ACMGNot met: missense-path REVEL score 0.549 exceeds the BP4 supporting threshold of 0.29. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, so the governing generic path is REVEL only; SpliceAI is not used for BP4 in this situation. REVEL is 0.549, above the generic BP4 supporting threshold of <= 0.29 (ClinGen SVI REVEL calibration, PMID:36413997), so BP4 is not met; the result is not a gray-zone basis for substituting SpliceAI.

Rule
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
Evidence considered
  • Variant consequence: missense, NP_000401.1:p.(Ser65Cys); therefore the generic missense path uses REVEL only.
  • Local REVEL lookup reports score 0.549 for NM_000410.4:c.193A>T.
  • The supplied ClinGen SVI REVEL calibration sets BP4 supporting at <= 0.29; this threshold is attributed to Pejaver et al. 2022, PMID:36413997.
  • SpliceAI max delta 0.028 was not counted because a splice prediction cannot provide BP4 support for a missense variant; BayesDel was not used because no generic ACMG-strength calibration is established.
Sources
revel
BP6 ACMG_2015Not met: ClinVar reports zero exact-variant expert-panel submissions, so single-laboratory Benign labels cannot support BP6. Details ▾Hide ▴
Reasoning

Generic ACMG/AMP BP6 requires a reputable source to report the variant as benign when the evidence is not available to the laboratory for independent evaluation. ClinVar has no exact-variant expert-panel classification for HFE NM_000410.4:c.193A>T (p.Ser65Cys); expert-panel submissions are zero. The available Benign and Likely benign assertions are single-submitter laboratory submissions, not expert-panel classifications, and therefore do not qualify for BP6 under the requested rule.

Rule
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
  • ClinVar exact-variant record NM_000410.4(HFE):c.193A>T (p.Ser65Cys), variation ID 11: expert-panel submissions = 0; overall classification is conflicting.
  • The available Benign and Likely benign classifications are single-submitter clinical laboratory assertions and are excluded from BP6 by the requested expert-panel-only rule.
Sources

Not assessed · 11 · no assessment recorded

PS2 ACMG_2015Not assessed: no documented de novo occurrence with confirmed maternity and paternity, disease phenotype, and no family history is available. Details ▾Hide ▴
Reasoning

No case-level evidence documents a patient with the disease carrying HFE NM_000410.4:c.193A>T as a de novo variant, and no maternity and paternity confirmation or absence of family history is provided. The available literature concerns population, genotype-phenotype, or family-screening observations rather than a confirmed de novo occurrence.

Rule
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Evidence considered
  • No proband-level de novo report, parental genotype results, maternity confirmation, paternity confirmation, or family-history statement was identified in the reviewed case evidence.
  • The available HFE S65C publications describe cohort and family-screening observations, not a confirmed de novo event for this variant (PMID:12377814; PMID:11943417).
Still missing
  • A case report or pedigree documenting the variant in an affected patient is needed.
  • Both maternity and paternity confirmation and an explicit absence of family history are needed for PS2.
PS3 ACMG_2015Not assessed: reviewed studies provide clinical observations but no validated in vitro or in vivo assay demonstrating a damaging effect of HFE p.Ser65Cys. Details ▾Hide ▴
Reasoning

The reviewed HFE S65C literature reports clinical cohorts, genotype-phenotype associations, and a review statement that the substitution has no evident effect on HFE protein structure, but it does not provide a validated, reproducible in vitro or in vivo functional assay demonstrating a damaging effect for this variant. The PS3 evidence requirement is therefore not satisfied and cannot be calibrated to any strength.

Rule
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Evidence considered
  • Le Gac and Ferec, PMID:16132052, review of HFE S65C literature: describes no evident effect on HFE protein structure and summarizes mild iron-overload associations, but the quoted passage is not a direct functional assay.
  • Holmstrom et al., PMID:12377814: retrospective study of 250 healthy controls and 296 patients with suspected iron overload using genotyping, biochemical indices, liver biopsy, and phlebotomy; this is clinical phenotype evidence rather than a validated protein-function assay.
  • Wallace et al., PMID:11943417: cohort study of 309 C282Y-heterozygous individuals assessing iron indices and hepatic iron; this is genotype-phenotype evidence rather than a variant-specific functional assay.
Still missing
  • A variant-specific, well-established in vitro or in vivo functional assay with appropriate controls and demonstrated reproducibility is not available in the reviewed evidence.
Sources
PM3 ACMG_2015Not assessed: 12 C282Y/S65C compound heterozygotes were reported, but parental or offspring testing to establish trans phase was not documented. Details ▾Hide ▴
Reasoning

HFE-related hemochromatosis is described as recessive, and PMID:11943417 reports 12 individuals with the target S65C variant and C282Y as compound heterozygotes; five had elevated serum iron indices and three had elevated hepatic iron. However, the extracted report does not document parental or offspring testing establishing phase, which is required by the governing rule. PMID:16132052 likewise describes S65C-associated mild iron overload when inherited with C282Y in the compound-heterozygous state but is a review and does not provide qualifying phase-testing details for these observations. Therefore PM3 cannot be assessed from the available evidence.

Rule
For recessive disorders, detected in trans with a pathogenic variant ... This requires testing of parents (or offspring) to determine phase.
Evidence considered
  • Wallace et al. 2002 (PMID:11943417), abstract/Results/Table 1: 12 individuals were compound heterozygotes for C282Y and S65C; 7 had normal serum iron indices, 5 had elevated serum iron indices, and 3 had elevated hepatic iron and received treatment.
  • Le Gac and Ferec 2005 (PMID:16132052), subsection 'S65C missense mutation,' page 1174: S65C is associated with mild iron-overload phenotypes when inherited with C282Y in the compound-heterozygous state; the review characterizes S65C as a risk factor rather than a causative mutation.
  • Neither extracted source documents parental or offspring testing used to establish phase for the reported observations.
Still missing
  • Documented parental or offspring testing establishing that HFE c.193A>T (p.Ser65Cys) is in trans with pathogenic C282Y in affected individuals.
Sources
PM6 ACMG_2015Not assessed: no affected proband with assumed de novo HFE c.193A>T and incomplete parental confirmation is documented. Details ▾Hide ▴
Reasoning

No case-level evidence documents HFE NM_000410.4:c.193A>T as assumed de novo in an affected patient. The available publications do not provide a proband-parent genotype configuration supporting de novo status without parental confirmation.

Rule
Assumed de novo, but without confirmation of paternity and maternity.
Evidence considered
  • No proband-parent genotype data or report of assumed de novo HFE c.193A>T was identified in the reviewed case evidence.
  • PMID:12377814 and PMID:11943417 describe inherited C282Y/S65C compound heterozygotes and family-screening observations, not assumed de novo occurrence.
Still missing
  • An affected proband with the variant and parental testing showing absence in at least one unconfirmed parent is needed.
  • The evidence must distinguish assumed de novo status from an inherited variant.
PP1 ACMG_2015Not assessed: family data include six S65C-carrying relatives and 12 C282Y/S65C individuals but do not demonstrate co-segregation in multiple affected family members. Details ▾Hide ▴
Reasoning

The available HFE S65C literature includes relatives and family-screening observations, but it does not establish co-segregation of this variant with disease in multiple affected family members. PMID:12377814 reports six S65C-carrying relatives and two C282Y/S65C brothers with differing iron findings; PMID:11943417 reports 12 C282Y/S65C individuals, including seven with normal indices and five with elevated indices, without a qualifying multigenerational segregation analysis. Therefore PP1 cannot be applied from these data.

Rule
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.
Evidence considered
  • Holmström et al. (PMID:12377814), Table 7 and family results: six S65C-carrying relatives were examined; one was S65C homozygous with iron deficiency, while the others lacked biopsy-confirmed hepatic findings; two brothers with C282Y/S65C had different iron indices, with one showing grade 1 liver iron staining.
  • Wallace et al. (PMID:11943417), abstract/results: 12 C282Y/S65C compound heterozygotes included seven with normal serum iron indices and five with elevated indices; these are cohort observations, not a qualifying segregation analysis across multiple affected family members.
  • These reports do not provide a pedigree demonstrating that HFE c.193A>T tracks with disease in multiple affected relatives.
Still missing
  • A pedigree with individual-level HFE c.193A>T genotypes and disease phenotypes is needed.
  • Multiple affected relatives carrying the variant, with adequate phenotyping and inheritance context, are needed to establish co-segregation.
Sources
PP4 ACMG_2015Not assessed: the case phenotype and family history are unavailable, so specificity for a single genetic etiology cannot be judged. Details ▾Hide ▴
Reasoning

Generic ACMG/AMP PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The available evidence describes study cohorts with suspected iron overload and variable HFE S65C-associated findings, including normal indices in some carriers and mild findings in others, but it does not provide this case's phenotype or family history and does not establish a single-gene-specific phenotype for HFE S65C. A case-level phenotype and family-history assessment is required.

Rule
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Evidence considered
  • Holmström et al. 2002: among 14 S65C-carrying patients, 7/14 were classified as having iron overload; biopsy findings were generally mild or moderate, and one S65C homozygous relative had iron deficiency.
  • Wallace et al. 2002: among 12 C282Y/S65C compound heterozygotes, 7 had normal serum iron indices and 5 had elevated indices, demonstrating variable expressivity.
  • Le Gac and Ferec 2005: S65C is described as a risk factor rather than a causative mutation.
Still missing
  • Case-level phenotype and family history, including biochemical and clinical evidence of HFE-related disease, are not available for PP4 assessment.
Sources
BS1 ACMGNot assessed: grpmax FAF is 1.61% above the 1% default, but HFE S65C has reduced, variable penetrance and no maximum-credible-frequency inputs are available. Details ▾Hide ▴
Reasoning

The frequency component exceeds the generic default: gnomAD v4.1 grpmax FAF=0.0160786 and v2.1 grpmax FAF=0.0149203, with qualifying population allele counts above 2000 for the FAF-bearing population. However, BS1 is a disorder-specific maximum-credible-frequency judgment, not an automatic 1% rule. HFE-related hemochromatosis is late-onset/reduced-penetrance, and S65C is reported as a common risk factor rather than a fully penetrant causative allele. The case does not provide disease prevalence, penetrance, allelic heterogeneity, or other inputs needed for a defensible Whiffin maximum-credible-frequency calculation; therefore the generic default alone is insufficient.

Rule
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168) ... the criterion is 'allele frequency is greater than expected for the disorder'
Evidence considered
  • gnomAD v2.1 grpmax FAF=0.0149203 and gnomAD v4.1 grpmax FAF=0.0160786; these are filtering allele frequencies, not popmax point estimates.
  • The relevant gnomAD v2.1 Finnish population has 25,120 observed alleles and the v4.1 non-Finnish European population has 1,180,008 observed alleles; the v4.1 Amish popmax has only 910 alleles and was not used for the threshold decision.
  • The molecular genetics of haemochromatosis (PMID:16132052) reports S65C as a risk factor rather than a causative mutation and describes mild iron-overload phenotypes in some compound-heterozygous contexts, supporting reduced or variable penetrance rather than full penetrance.
  • Whiffin et al. 2017 (PMID:28518168) is the named source for evaluating a disorder-specific maximum credible allele frequency; the required prevalence, penetrance, and allelic-heterogeneity inputs are not available in this case.
Still missing
  • A defensible maximum credible allele frequency requires disease prevalence, penetrance, allelic heterogeneity, and inheritance-model inputs for the specific HFE-related disorder.
  • The generic 1% default cannot be used alone for this reduced-penetrance, late-onset risk allele.
Sources
BS3 ACMG_2015Not assessed: reviewed studies provide clinical observations but no well-established assay showing that HFE p.Ser65Cys has no damaging effect on protein function or splicing. Details ▾Hide ▴
Reasoning

The reviewed HFE S65C literature includes clinical phenotype studies and a review statement that the substitution has no evident effect on HFE protein structure, but it does not provide a well-established in vitro or in vivo assay showing no damaging effect on protein function or splicing. The BS3 evidence requirement is therefore not satisfied and cannot be calibrated to any strength.

Rule
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Evidence considered
  • Le Gac and Ferec, PMID:16132052, review of HFE S65C literature: states that the mutation produces no evident effect on HFE protein structure, but this is a review conclusion and not a well-established direct assay of protein function or splicing.
  • Holmstrom et al., PMID:12377814: clinical study of S65C carriers with iron indices, liver biopsy, and treatment outcomes; it does not establish normal HFE protein function or normal splicing.
  • Wallace et al., PMID:11943417: clinical genotype-phenotype cohort with variable iron-overload findings; it does not establish absence of a damaging molecular effect.
Still missing
  • A well-established variant-specific functional or splicing assay with appropriate controls demonstrating no damaging effect is not available in the reviewed evidence.
Sources
BS4 ACMG_2015Not assessed: no affected-family-member dataset shows absence of HFE c.193A>T, and phenocopies or additional pathogenic variants cannot be evaluated. Details ▾Hide ▴
Reasoning

No family-level dataset documents affected relatives who lack HFE NM_000410.4:c.193A>T, and no validated non-segregation analysis is available. The available family and cohort observations are insufficient to establish lack of segregation; the BS4 caveat also requires consideration of phenocopies and families with more than one pathogenic variant.

Rule
Lack of segregation in affected members of a family. ... Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, fu
Evidence considered
  • No affected-family-member genotype data demonstrating absence of HFE c.193A>T were identified in the reviewed case evidence.
  • The available family-screening and cohort papers do not provide a validated non-segregation analysis for this variant (PMID:12377814; PMID:11943417).
Still missing
  • A pedigree identifying affected relatives, their HFE c.193A>T genotypes, and phenotype definitions is needed.
  • Potential phenocopies and additional pathogenic variants in the family must be evaluated before concluding lack of segregation.
BP2 ACMG_2015Not assessed: reported C282Y/S65C observations are compound heterozygotes, with no cis observation and no fully penetrant dominant HFE disorder established. Details ▾Hide ▴
Reasoning

The available evidence reports S65C with C282Y in compound-heterozygous individuals, not a cis observation. The governing BP2 rule allows a trans observation only for a fully penetrant dominant gene/disorder, whereas HFE-related hemochromatosis is described in the case literature as recessive; no cis pathogenic-variant observation for HFE c.193A>T was identified. Because the available evidence does not establish either qualifying BP2 configuration, BP2 is not assessed.

Rule
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Evidence considered
  • Wallace et al. 2002 (PMID:11943417), abstract/Results: the target S65C variant was reported with C282Y as a compound-heterozygous genotype; no cis configuration was reported in the extracted finding.
  • Le Gac and Ferec 2005 (PMID:16132052), subsection 'S65C missense mutation,' page 1174: S65C was discussed in the compound-heterozygous state with C282Y and as a recessive-disease risk factor, not as evidence for a fully penetrant dominant disorder.
  • No extracted source documents a qualifying cis observation or a fully penetrant dominant HFE disorder for this variant.
Still missing
  • Direct evidence of HFE c.193A>T in cis with a pathogenic HFE variant, or evidence establishing a fully penetrant dominant HFE disorder with the target variant in trans.
Sources
BP5 ACMG_2015Not assessed: no case-level evidence shows an alternate molecular basis for the patient's disease. Details ▾Hide ▴
Reasoning

Generic ACMG/AMP BP5 requires the variant to be found in a case with an alternate molecular basis for disease. The available HFE S65C literature describes variable iron-overload phenotypes and comparator genotypes, but does not document that this case has an alternate molecular diagnosis explaining its disease. Case-level molecular and clinical information is required.

Rule
Variant found in a case with an alternate molecular basis for disease.
Evidence considered
  • The reviewed HFE S65C studies report cohort phenotypes and other HFE genotypes but do not establish an alternate molecular basis for this case.
Still missing
  • Case-level molecular diagnosis and clinical documentation establishing an alternate cause of disease are not available.
Sources
Not applicable · 4· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANot applicable: PVS1 requires a null variant (nonsense, frameshift, canonical splice, start-loss or stop-loss), and this is a missense variant. Details ▾Hide ▴
Reasoning

PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_000410.4:c.193A>T in HFE is a missense substitution predicted to produce NP_000401.1:p.(Ser65Cys). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for HFE, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_null_variant_class
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
PM4 N/ANot applicable: PM4 requires a protein-length change, and this is a missense variant. Details ▾Hide ▴
Reasoning

PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_000410.4:c.193A>T in HFE is a missense substitution predicted to produce NP_000401.1:p.(Ser65Cys). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for HFE, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
BP3 N/ANot applicable: BP3 requires an in-frame indel in a repeat region, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000410.4:c.193A>T in HFE is a missense substitution predicted to produce NP_000401.1:p.(Ser65Cys). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for HFE, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_repeat_region_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000410.4:c.193A>T in HFE is a missense substitution predicted to produce NP_000401.1:p.(Ser65Cys). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for HFE, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Identifiers

Gene
HFE
Transcript
NM_000410.4
Coding (HGVS c.)
NM_000410.4:c.193A>T
Protein (HGVS p.)
NP_000401.1:p.(Ser65Cys)
GRCh38
chr6:26090957 A>T
GRCh37
chr6:26091185 A>T
Location and type
Exon 2 · missense
ClinVar
1185560, 11

Gene diagram

Every interpreted variant in HFE, mapped onto the exon structure of NM_000410.4. Select a row to find it on the plot.

HFENM_000410.4
Fetching transcript structure from UCSC…
gnomAD v4.1 22,016 / 1,614,088 alleles AF 0.0136 · 195 homozygotes · FAF 0.0161
gnomAD v2.1 2,891 / 282,878 alleles AF 0.0102 · 24 homozygotes · FAF 0.0149
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 0.014 · 22016 / 1,614,088 alleles · 195 hom · FAF 0.016
Amish24 / 910 0.026
European (Finnish)1415 / 64,016 0.02227 hom
European (non-Finnish)19201 / 1,180,008 0.016159 hom
Remaining individuals679 / 62,508 0.0114 hom
Admixed American314 / 60,018 0.00523 hom
Ashkenazi Jewish89 / 29,604 0.003
African/African American190 / 75,012 0.00251 hom
Middle Eastern6 / 6,060 0.00099
South Asian90 / 91,080 0.000991 hom
East Asian8 / 44,872 0.00018

gnomAD v2.1

AF 0.01 · 2891 / 282,878 alleles · 24 hom · FAF 0.015
European (Finnish)537 / 25,120 0.0219 hom
European (non-Finnish)1977 / 129,196 0.01514 hom
Remaining individuals72 / 7,226 0.011 hom
Admixed American173 / 35,440 0.0049
Ashkenazi Jewish35 / 10,370 0.0034
African/African American63 / 24,958 0.0025
South Asian30 / 30,616 0.00098
East Asian4 / 19,952 0.0002

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.0136399; MAF= 1.36399%, 22016/1614088 alleles, homozygotes = 195) and has highest observed frequency in the Amish population (AF= 0.0263736; MAF= 2.63736%, 24/910 alleles, homozygotes = 0); grpmax FAF= 0.0160786.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.01022; MAF= 1.02200%, 2891/282878 alleles, homozygotes = 24) and has highest observed frequency in the European (Finnish) population (AF= 0.0213774; MAF= 2.13774%, 537/25120 alleles, homozygotes = 9); grpmax FAF= 0.0149203.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -116 bp
0.014
SpliceAI acceptor gainat -340 bp
0.000
SpliceAI donor lossat +147 bp
0.028
SpliceAI donor gainat -2 bp
0.000
Pangolin splice lossmagnitude shown
-0.022
Pangolin splice gain
0.002

Other predictors

REVEL
0.549
BayesDel
0.106

How the predictions were used

PP3 ACMGNot met: missense-path REVEL score 0.549 is below the PP3 supporting threshold of 0.644. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, so the governing generic path is REVEL only; SpliceAI and BayesDel are not used for PP3 in this situation. REVEL is 0.549, below the generic PP3 supporting threshold of >= 0.644 (ClinGen SVI REVEL calibration, PMID:36413997), so PP3 is not met.

Rule
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Evidence considered
  • Variant consequence: missense, NP_000401.1:p.(Ser65Cys); therefore the generic missense path uses REVEL only.
  • Local REVEL lookup reports score 0.549 for NM_000410.4:c.193A>T.
  • The supplied ClinGen SVI REVEL calibration sets PP3 supporting at >= 0.644; this threshold is attributed to Pejaver et al. 2022, PMID:36413997.
  • SpliceAI max delta 0.028 and BayesDel 0.105529 were not counted because they are not the governing predictor path for a missense PP3 assessment; BayesDel has no established generic ACMG-strength calibration.
Sources
revel
BP4 ACMGNot met: missense-path REVEL score 0.549 exceeds the BP4 supporting threshold of 0.29. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, so the governing generic path is REVEL only; SpliceAI is not used for BP4 in this situation. REVEL is 0.549, above the generic BP4 supporting threshold of <= 0.29 (ClinGen SVI REVEL calibration, PMID:36413997), so BP4 is not met; the result is not a gray-zone basis for substituting SpliceAI.

Rule
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
Evidence considered
  • Variant consequence: missense, NP_000401.1:p.(Ser65Cys); therefore the generic missense path uses REVEL only.
  • Local REVEL lookup reports score 0.549 for NM_000410.4:c.193A>T.
  • The supplied ClinGen SVI REVEL calibration sets BP4 supporting at <= 0.29; this threshold is attributed to Pejaver et al. 2022, PMID:36413997.
  • SpliceAI max delta 0.028 was not counted because a splice prediction cannot provide BP4 support for a missense variant; BayesDel was not used because no generic ACMG-strength calibration is established.
Sources
revel
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000410.4:c.193A>T in HFE is a missense substitution predicted to produce NP_000401.1:p.(Ser65Cys). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for HFE, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.549. BayesDel score = 0.105529.

10 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.

Recorded publications

  • The molecular genetics of haemochromatosis.
    Le Gac G et al. · 2005
    The paper explicitly describes the HFE 193 A>T transversion, producing the S65C missense substitution (equivalent to c.193A>T and p.(S65C)). It reports a frequency of 1.6–5.5% on Caucasian chromosomes, no evident effect on HFE protein structure, enrichment on affected chromosomes lacking C282Y and H63D, and association with mild iron-overload phenotypes when inherited with C282Y in the compound-heterozygous state. The authors describe S65C as a risk factor rather than a causative mutation.
    Names this variant
    PMID 16132052 ↗
    Quoted passage
    The 193 A4T transversion, which leads to the serine 65 to cysteine substitution (S65C), displays a frequency ranging from 1.6 to 5.5% on Caucasian chromosomes. This mutation produces no evident effect on the HFE protein structure, but we and others have found that it is significantly enriched on affected chromosomes that carry neither the C282Y nor the H63D mutation. Moreover, it is associated with mild iron overload phenotypes when inherited with the predominant C282Y mutation in the compound heterozygous state. As with the H63D mutation, the S65C mutation should be considered as a risk factor rather than as a causative mutation

    Haemochromatosis type 1 – HFE related; subsection ‘Other HFE genotypes related to iron overload phenotypes,’ subsection ‘S65C missense mutation,’ page 1174

  • EFNS guidelines for the diagnosis and management of Alzheimer's disease.
    No paper-specific finding is recorded.
    PMID 20831773 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • HFE mutations analysis in 711 hemochromatosis probands: evidence for S65C implication in mild form of hemochromatosis.
    Mura C et al. · 1999
    No paper-specific finding is recorded.
    PMID 10194428 ↗
  • HFE S65C variant is not associated with increased transferrin saturation in voluntary blood donors.
    Arya N et al. · 1999
    No paper-specific finding is recorded.
    PMID 10660483 ↗
  • Diagnosis of hemochromatosis in family members of probands: a comparison of phenotyping and HFE genotyping.
    No paper-specific finding is recorded.
    PMID 11336458 ↗
  • Frequency of the S65C mutation of HFE and iron overload in 309 subjects heterozygous for C282Y.
    Wallace DF et al. · 2002
    The paper explicitly studied HFE S65C (the same variant as NP_000401.1:p.(S65C), c.193A>T) in 309 individuals heterozygous for C282Y and negative for H63D. Twelve were C282Y/S65C compound heterozygotes. Seven had normal serum iron indices, while five had elevated serum iron indices; three had elevated hepatic iron and received treatment for iron overload. In the Australian subgroup, S65C-positive C282Y heterozygotes had higher transferrin saturation than S65C-negative C282Y heterozygotes (mean 47% vs 28%, P=0.013), whereas the ferritin difference was not statistically significant. The authors reported a range of findings from severe iron overload to no iron overload and noted that other genetic or environmental factors may influence expression.
    Names this variant
    PMID 11943417 ↗
    Quoted passage
    Twelve individuals were compound heterozygotes for C282Y and S65C. Seven, referred for family screening, had normal serum iron indices. Five subjects had elevated serum iron indices; three of these had elevated hepatic iron and have received treatment for iron overload.

    Abstract, Results; Table 1; Discussion

  • Mild iron overload in patients carrying the HFE S65C gene mutation: a retrospective study in patients with suspected iron overload and healthy controls.
    Holmström P et al. · 2002
    The paper explicitly studied the HFE S65C variant, corresponding to NP_000401.1:p.(S65C) and c.193A>T. In 250 healthy controls, S65C was found in 8 individuals, with an allele frequency of 1.6%; in 296 patients evaluated for suspected iron overload, it was found in 14 individuals, and its frequency on chromosomes lacking C282Y or H63D was 4.9% versus 1.9% in controls. Among the 14 S65C-carrying patients, 7/14 were classified as having iron overload; 7 underwent liver biopsy, 6 showed mild or moderate hepatic iron deposition (HIS grade 1 or 2), and none had extensive fibrosis. Six patients received phlebotomy, with 1.9–8.0 litres removed until ferritin normalized. Six relatives carrying S65C were also examined: one was S65C homozygous and had iron deficiency, while the others had no biopsy-confirmed hepatic findings; one had increased ferritin and two had increased transferrin saturation. The paper also reports two brothers with C282Y/S65C who had different iron indices, with one showing grade 1 liver iron staining. The study used RFLP and confirmatory sequencing for controls and automated DNA sequencing for patients.
    Names this variant
    PMID 12377814 ↗
    Quoted passage
    The HFE S65C mutation was found in 14 patients and eight controls. In controls, the S65C allele frequency was 1.6%. The S65C allele frequency was enriched in non-C282Y non-H63D chromosomes from patients (4.9%) compared with controls (1.9%) (p<0.05).

    Abstract, Results; Table 2; Table 4; Table 5; Table 7

  • Screening for hemochromatosis: recommendation statement.
    No paper-specific finding is recorded.
    PMID 16880462 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    No paper-specific finding is recorded.
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.0136399; MAF= 1.36399%, 22016/1614088 alleles, homozygotes = 195) and has highest observed frequency in the Amish population (AF= 0.0263736; MAF= 2.63736%, 24/910 alleles, homozygotes = 0); grpmax FAF= 0.0160786.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.01022; MAF= 1.02200%, 2891/282878 alleles, homozygotes = 24) and has highest observed frequency in the European (Finnish) population (AF= 0.0213774; MAF= 2.13774%, 537/25120 alleles, homozygotes = 9); grpmax FAF= 0.0149203.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories) and as Likely benign (4 clinical laboratories) and as Benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 11)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.549. BayesDel score = 0.105529.

Functional

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. HFE, a transmembrane protein, is altered by mutation in various cancers. Germline HFE mutations are associated with hemochromatosis and predispose to

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.