Variant classification summary

NM_000143.4:c.301C>T

FH · NP_000134.2:p.(Arg101Ter) · NM_000143.4

GRCh37: chr1:241676980 G>A · GRCh38: chr1:241513680 G>A

Gene: FH Transcript: NM_000143.4

Final call

Pathogenic

PVS1 very strong PS3 supporting PM2 moderate PP5 supporting

Variant details

Gene

FH

Transcript

NM_000143.4

Protein

NP_000134.2:p.(Arg101Ter)

gnomAD AF

7.435404919759588e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000143.4:c.301C>T (p.Arg101Ter) is a nonsense variant in exon 3 of 10 in the FH gene, which encodes fumarate hydratase. Loss-of-function variants in FH are an established cause of autosomal dominant hereditary leiomyomatosis and renal cell cancer (HLRCC).

2

This variant introduces a premature termination codon at position 101 of 511 amino acids, predicted to trigger nonsense-mediated decay and result in complete loss of protein function. Under ClinGen SVI PVS1 guidelines, this meets criteria for PVS1 at very strong strength.

3

The variant is absent from gnomAD v2.1 and gnomAD-Canada, and is present at extremely low frequency in gnomAD v4.1 (12/1,613,900 alleles, AF = 0.00074%, no homozygotes), meeting PM2 at moderate strength.

4

Protein-truncating FH mutations have been demonstrated to be functionally null alleles in published studies, and OncoKB annotates R101* as Likely Loss-of-function, supporting a damaging functional effect at PS3 supporting strength.

5

This variant has been classified as Pathogenic by 14 clinical laboratories in ClinVar (Variation ID 16232) and is annotated as Likely Oncogenic by OncoKB, meeting PP5 at supporting strength.

6

No benign criteria are met. The variant is absent or at extremely low frequency in population databases (BA1/BS1 not met), functional evidence supports a damaging effect (BS3 not met), and no reputable source reports this variant as benign (BP6 not met).

7

Applying the ACMG/AMP 2015 combination rules: 1 Very Strong (PVS1) + 1 Moderate (PM2) + 2 Supporting (PS3, PP5) satisfies the threshold for Pathogenic classification.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	Null variant (nonsense) in gene FH where loss of function is a known mechanism of disease for hereditary leiomyomatosis and renal cell cancer (HLRCC). The variant introduces a premature termination codon at position 101 of 511 amino acids in exon 3 of 10, predicted to trigger nonsense-mediated decay. FH is an established tumor suppressor with autosomal dominant HLRCC predisposition; truncating germline FH variants are a well-characterized cause of this syndrome. Per ClinGen SVI PVS1 recommendations (PMC6185798), a nonsense variant in a gene with established LoF disease mechanism is assigned PVS1 at full strength.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment
PS1	N/A	PS1 applies when a different nucleotide change at the same codon produces the same missense amino acid change that is already established as pathogenic. This variant is a nonsense (stop-gain) change, not a missense variant, so PS1 is not applicable.
PS2	Not assessed	No de novo observation with confirmed paternity and maternity was identified in the available evidence. No full-text publications mentioning this specific variant were available for review.
PS3	Met	Protein-truncating FH mutations have been demonstrated to be functionally null alleles. PMID:12761039 states that 'Protein-truncating FH mutations are functionally null alleles,' and multiple studies (PMID:16597677, PMID:21398687) have demonstrated significantly reduced FH enzymatic activity in cells from HLRCC patients harboring various FH mutations. OncoKB annotates this variant as 'Likely Loss-of-function.' While no full-text publication specifically assaying the R101* variant was identified, the functional null effect of nonsense variants in FH is well-established across the literature. The strength is downgraded to supporting because the evidence is derived from class-level functional characterization rather than a variant-specific assay.	PMID:12761039 PMID:16597677 PMID:21398687 oncokb
PS4	Not assessed	No formal case-control study or statistically significant enrichment data specific to NM_000143.4:c.301C>T was identified in the available evidence. ClinVar reports this variant as Pathogenic by 14 clinical laboratories, suggesting multiple independent observations, but without formal case-control statistics this does not satisfy PS4.
PS5	Not assessed	PS5 requires an established pathogenic variant at the same nucleotide position (typically a different nucleotide change at the same genomic coordinate). No such comparator was identified for c.301 in the available evidence.
PM1	Not met	The variant is not located in a recognized mutational hotspot for FH. Cancer Hotspots does not list residue R101 as a statistically significant hotspot. Published data (PMID:41496563) identifies exons 5 and 7 in the fumarate lyase domain as the predominant FH mutational hotspots, while c.301C>T is in exon 3. Although the variant lies within the fumarate lyase domain broadly, the absence of hotspot-level mutation clustering at this residue precludes application of PM1.	hotspots
PM2	Met	The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0, and is present at extremely low frequency in gnomAD v4.1 (12/1,613,900 alleles, global AF = 0.00074%), all observed in the European (non-Finnish) population (12/1,179,948, subpopulation AF = 0.00102%). This frequency is well below the 0.1% threshold for PM2 in non-VCEP assessment. No homozygotes are observed.	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	PM3 applies to recessive disorders where the variant is observed in trans with a pathogenic variant. FH-associated HLRCC is an autosomal dominant disorder, so PM3 is not applicable.
PM4	N/A	PM4 applies to in-frame deletions/insertions in a non-repeat region or stop-loss variants that alter protein length. This is a nonsense (stop-gain) variant creating a truncated protein, not an in-frame change or stop-loss variant, so PM4 is not applicable.
PM5	N/A	PM5 applies to a novel missense change at an amino acid residue where a different missense change has been determined to be pathogenic. This is a nonsense variant (R101*), not a missense change. Automated PM5 candidate harvesting was unable to identify eligible same-residue comparators under classic PM5 semantics.	pm5_candidates
PM6	Not assessed	No de novo observation (without confirmed paternity and maternity) was identified for this variant in the available evidence. PM6 requires a de novo observation without parental confirmation; no such data was found.
PP1	Not assessed	No co-segregation data for NM_000143.4:c.301C>T with disease in multiple affected family members was identified in the available evidence.
PP2	N/A	PP2 applies to missense variants in a gene with a low rate of benign missense variation (high missense constraint). This is a nonsense (truncating) variant, not a missense variant, so PP2 is not applicable.
PP3	Not met	Insufficient computational evidence to support a deleterious effect. SpliceAI predicts no splice-altering impact (max delta score = 0.00). BayesDel score is borderline at 0.486, below typical deleterious thresholds. REVEL is unavailable for this variant. No multiple lines of in silico evidence converge on a deleterious prediction to satisfy PP3.	spliceai bayesdel
PP4	Not assessed	No patient-specific phenotype or family history data were available for review. PP4 requires a phenotype or family history highly specific for a disease with a single genetic etiology; this cannot be evaluated without clinical context.
PP5	Met	Multiple reputable clinical laboratories and curated databases report NM_000143.4:c.301C>T as pathogenic. ClinVar records 14 clinical laboratories classifying this variant as Pathogenic (Variation ID 16232, review status: criteria provided, single submitter). Three major clinical testing laboratories (Ambry Genetics, Invitae/Labcorp, Fulgent Genetics) and OMIM have submitted Pathogenic classifications. OncoKB annotates this variant as Likely Oncogenic with a Likely Loss-of-function biological effect. While the evidence underlying these classifications could not be independently verified, the consensus from multiple reputable sources supports application of PP5.	clinvar oncokb
BA1	Not met	The variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF = 0.00074%). BA1 requires an allele frequency >5% in population databases, which is not met.	gnomad_v4
BS1	Not met	The variant is present in gnomAD v4.1 at a global AF of 0.00074% (grpmax FAF = 5.42e-06). For non-VCEP assessment, the BS1 threshold is >0.3%. The observed frequency is far below this threshold, so BS1 is not met.	gnomad_v4
BS2	Not met	The variant is observed in gnomAD v4.1 at very low frequency (12/1,613,900 alleles, all in the NFE population, 0 homozygotes). However, HLRCC is an adult-onset disorder (cutaneous/uterine leiomyomas and renal cell cancer typically manifest in adulthood), so observation in a general population database where individuals may not have reached the age of disease penetrance does not constitute convincing evidence for BS2. BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age.	gnomad_v4
BS3	Not met	BS3 requires well-established functional studies showing no damaging effect on protein function or splicing. The available functional evidence for FH truncating variants consistently supports a damaging (loss-of-function) effect, not a benign effect. BS3 is not met.	PMID:12761039 PMID:16597677 PMID:21398687
BS4	Not assessed	No segregation data were available to assess lack of co-segregation with disease in affected family members. BS4 cannot be evaluated without family-level segregation analysis.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. This is a nonsense (truncating) variant, so BP1 is not applicable.
BP2	Not assessed	No data were available regarding observation of this variant in trans with a known pathogenic FH variant. BP2 applies to variants observed in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP3	N/A	BP3 applies to in-frame deletions or insertions in a repetitive region without a known function. This is a single-nucleotide substitution resulting in a nonsense change, so BP3 is not applicable.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product. SpliceAI predicts no splice impact (max delta = 0.00), which is one line of non-damaging evidence. However, BayesDel is borderline (0.486) and REVEL is unavailable, so there are not multiple lines of computational evidence converging on a benign prediction. A single non-damaging SpliceAI score is insufficient for BP4.	spliceai bayesdel
BP5	Not assessed	No data were available regarding observation of this variant in a case with an alternate molecular basis for disease. BP5 cannot be evaluated without case-level molecular data.
BP6	Not met	BP6 requires a reputable source to report the variant as benign. All available ClinVar submissions classify this variant as Pathogenic; OncoKB classifies it as Likely Oncogenic. No reputable source reports this variant as benign, so BP6 is not met.	clinvar oncokb
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact on the splice consensus sequence or splicing efficiency. This variant is a nonsense (stop-gain) change, not a synonymous variant, so BP7 is not applicable.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.