The MTHFR NM_005957.5:c.665C>T (NP_005948.3:p.(Ala222Val)) missense variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: P.Ala222Val showed approximately 30% homozygous enzyme activity and increased thermolability across expression and patient-fibroblast assays. Based on available guidelines, this variant is considered to be Benign. This variant is considered to be drug response by the VCEP (ClinPGx; ClinVar ID 3520).
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.MTHFR encodes an enzyme that helps process folate and supports the conversion of homocysteine into methionine, an essential building block for the body. Changes in this gene can cause methylenetetrahydrofolate reductase deficiency and may influence susceptibility to vascular disease and neural tube defects. MTHFR has been studied in colon cancer, acute leukemia, and other cancers, but there is insufficient evidence to classify it as an oncogene or tumor suppressor.
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.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met at supporting: p.Ala222Val showed approximately 30% homozygous enzyme activity and increased thermolability across expression and patient-fibroblast assays.
Met at moderate strength: missense REVEL score 0.842 meets the generic PP3 threshold of >=0.773 but is below the >=0.932 strong threshold.
Met: gnomAD allele frequency is 0.318214, far above the generic BA1 stand-alone threshold of 0.05.
Met: AF 0.318214 with 87,723 homozygotes is far above the generic BS1 default threshold of 0.01 and incompatible with a rare fully penetrant disorder.
Benign: BA1 stand-alone is met by the 0.318214 gnomAD allele frequency, with BS1 strong also applied; pathogenic evidence does not satisfy a pathogenic rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 513,548 / 1,613,846 alleles. Recorded AF 0.318214. Recorded homozygote count 87723.
This variant is present in gnomAD v2.1 (AF= 0.308483; MAF= 30.84828%, 87234/282784 alleles, homozygotes = 15819) and has highest observed frequency in the Admixed American population (AF= 0.501919; MAF= 50.19187%, 17788/35440 alleles, homozygotes = 4654); grpmax FAF= 0.496463.
This variant is present in gnomAD-Canada v1.0 (AF= 0.3201935624184428, 5889/18392 alleles, homozygotes = 1086).
Recorded REVEL score: 0.842. Refer to the recorded PP3/BP4 rationale for interpretation.
8 Benign · 3 Pathogenic · 3 Uncertain significance · 1 Likely benign · 1 Association · 1 other · 1 Likely Pathogenic. ClinVar API review status: reviewed by expert panel.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MTHFR, a reductase in the folate cycle, is altered in various cancers.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
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: 4 met · 10 not met · 10 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
PS2, PM6, PP1, and BS4 are all not assessed because the available case materials contain no proband-level de novo testing or family-level segregation/non-segregation data for NM_005957.5:c.665C>T.
Functional evidence supports PS3 at supporting strength because concordant biochemical, thermolability, expression, and patient-fibroblast findings indicate impaired MTHFR function, but clinical diagnostic laboratory validation is not established in the supplied evidence.
BS3 is not met because the available studies show reduced activity and thermolability rather than no damaging effect.
No VCEP covers MTHFR, so generic ACMG/AMP 2015 rules govern.
The available paper extracts document common C677T/A222V population, biochemical, functional, or treatment-toxicity observations, but do not establish PP4, BP5, or a qualifying PS4 case-control estimate.
ClinVar's exact-variant expert-panel classification is drug response, so it does not satisfy the required Pathogenic/Likely pathogenic PP5 or Benign/Likely benign BP6 trigger.
Generic ACMG/AMP rules govern because no VCEP covers MTHFR.
The variant is missense, so PP3 and BP4 use the REVEL path only; the available SpliceAI score is not counted for either criterion.
REVEL 0.842 meets PP3 moderate but not PP3 strong, and does not meet BP4 supporting.
Population evidence strongly supports a benign interpretation for this common MTHFR c.665C>T (p.Ala222Val) polymorphism: BA1 is met and BS1 is met, while PM2 is not met.
BS2 was not assessed because the available aggregate population data do not establish healthy-adult status, inheritance model, and early full penetrance as required by the criterion.
No criteria match.
PS3 is met at supporting strength. Multiple biologically relevant, variant-specific functional studies evaluate MTHFR p.Ala222Val (historical c.677C>T numbering). Frosst et al. demonstrated reduced MTHFR activity in homozygotes, reduced residual activity after heat treatment, and greater thermolability of mutagenized versus wild-type MTHFR expressed in E. coli, with genotype/activity and assay comparisons serving as controls. Subsequent work in patient fibroblast lysates found genotype-dependent thermolability (CC 42 ± 11%, CT 29 ± 14%, TT 21 ± 9% activity remaining after heat treatment), and recombinant MTHFR work identifies approximately 60% activity reduction in homozygotes. The concordant biochemical, stability, and cell-based findings support a damaging effect on protein function. Supporting rather than stronger calibration is appropriate because the supplied evidence does not demonstrate validation, reproducibility, and robustness in a clinical diagnostic laboratory setting.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
NM_005957.5:c.665C>T produces the missense substitution NP_005948.3:p.(Ala222Val). Under the generic rule, the missense path uses REVEL only; SpliceAI is not used for PP3/BP4 in this situation. The REVEL score is 0.842, which meets the supplied generic PP3 moderate threshold of >=0.773 but does not meet the strong threshold of >=0.932. Therefore PP3 is met at moderate strength. BayesDel has no established generic ACMG-strength calibration and is not used.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)....Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant....PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BA1 is met. The variant is common in both default all-comers gnomAD datasets: AF 0.308483 in gnomAD v2.1 (87,234/282,784 alleles) and AF 0.318214 in gnomAD v4.1 (513,548/1,613,846 alleles). The highest population frequencies are also far above the 5% stand-alone threshold, including 0.501919 in the gnomAD v2.1 Admixed American population and 0.483516 in the gnomAD v4.1 Amish population. The non-cancer subsets are concordant (0.314785 in gnomAD v2.1 non-cancer exomes and 0.274260 in gnomAD v3.1 non-cancer genomes), so cohort selection does not alter the conclusion.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
BS1 is met. The variant has AF 0.308483 in gnomAD v2.1 and 0.318214 in gnomAD v4.1, with 15,819 and 87,723 homozygotes, respectively; non-cancer datasets remain similarly high at AF 0.314785 in v2.1 exomes and 0.274260 in v3.1 genomes. These frequencies and homozygote counts are far above what would be expected for a rare, fully penetrant early-onset MTHFR deficiency disorder, even without relying solely on the 1% default. The result is not an ancestry-only elevation: multiple broad populations show high frequencies, including European non-Finnish AF 0.337103 in gnomAD v4.1 and East Asian AF 0.348436.
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
PS1 is not met. The variant is MTHFR NP_005948.3:p.(Ala222Val), but the reviewed evidence identifies this exact A222V change rather than a different nucleotide change producing the same amino-acid substitution; no previously established pathogenic same-amino-acid variant with an alternate nucleotide change is documented. PMID:12673793 and PMID:7647779 discuss the common 677C>T/A222V polymorphism, not an independent same-protein-change pathogenic comparator.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
PM1 is not met. PMID:12673793 places A222V within the MTHFR catalytic domain, but the generic PM1 requirement is a critical domain or hotspot without benign variation. This variant itself is common in population databases (gnomAD v4.1 AF 0.318214; 513548/1613846 alleles; 87723 homozygotes), so the required absence of benign variation is not satisfied. vcep_materials.json has no MTHFR domain-table entry and no VCEP-specific hotspot route applies.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PM2 is not met. The variant is not absent or extremely rare in controls; it occurs at AF 0.308483 in gnomAD v2.1 and AF 0.318214 in gnomAD v4.1, with concordant non-cancer frequencies of 0.314785 in v2.1 exomes and 0.274260 in v3.1 genomes. Each value is vastly above the generic PM2 supporting threshold of <=0.0001.
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
PM5 is not met. The observed substitution is Ala222Val, and the reviewed same-residue candidate collection contains no alternate missense change at Ala222 with an established pathogenic classification. The available publications describe A222V itself and do not establish a different pathogenic missense substitution at residue 222.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
PP2 is not met. The criterion requires both a low rate of benign missense variation and missense variants as a common disease mechanism. MTHFR has abundant benign missense variation: the observed A222V variant alone has gnomAD v4.1 AF 0.318214 with 87723 homozygotes, directly contradicting a low benign-missense-rate premise. The available evidence also documents the common A222V polymorphism as a frequent studied variant rather than establishing the required gene-level PP2 combination.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The exact-variant ClinVar expert-panel classification is drug response, not Pathogenic or Likely pathogenic. The Pathogenic and Likely pathogenic records are ordinary laboratory submissions or single-submitter assertions, which do not meet the required expert-panel condition for PP5.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BS3 is not met. The reviewed functional evidence does not show no damaging effect on MTHFR p.Ala222Val; instead, the reported biochemical and cellular assays show reduced enzyme activity and increased thermolability, including approximately 30% activity in homozygotes and 21% residual activity after heat treatment in TT fibroblast lines. No independent well-established assay demonstrating normal protein function or normal splicing for this variant was identified.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
BP1 is not met. MTHFR is not established here as a gene in which disease is caused primarily by truncating variants: the reviewed MTHFR deficiency literature describes multiple missense disease-associated mutations, while the common A222V missense variant is extensively characterized. Therefore the gene-level primarily-truncating premise of BP1 is not supported.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
NM_005957.5:c.665C>T is a missense variant, so BP4 must be assessed using REVEL only; the SpliceAI result cannot be substituted into the missense path. REVEL is 0.842, above the generic BP4 supporting threshold of <=0.29 and therefore in neither a BP4 range nor a benign computational range. BP4 is not met. BayesDel has no established generic ACMG-strength calibration and is not used.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)....Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant....BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
The exact-variant ClinVar expert-panel classification is drug response rather than Benign or Likely benign. Benign and Likely benign records in ClinVar are ordinary laboratory or non-expert submissions, so they cannot trigger BP6 under the required expert-panel restriction.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The case materials do not document a proband with a defined disease phenotype, confirmed maternity and paternity, a de novo genotype, or absence of family history for NM_005957.5:c.665C>T. Therefore the PS2 requirements cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The reviewed literature includes studies of the common MTHFR C677T/A222V polymorphism and genotype-associated biochemical or treatment-toxicity outcomes, but no accessible source supplies a qualifying affected-disease case count and matched unaffected/population-control count for this exact variant with which to calculate an OR and 95% CI. The literature_pass.json criteria index lists PMID:11710708, PMID:12915598, PMID:20301327, PMID:25394175, PMID:30247353, and PMID:35645034 as PS4 leads, but packet.ai_classified_papers is empty and none of those papers has a paper_extracts entry or available full text in this case, so those leads cannot be verified against an abstract or full text. gnomAD v4 reports a population allele frequency of 0.318214, but a population frequency alone is not a case-control comparison and cannot establish PS4.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... 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.
PM3 is relevant to the recessive MTHFR deficiency context, but the available evidence does not identify an affected proband carrying NM_005957.5:c.665C>T with a specified pathogenic MTHFR variant, nor does it establish that any such variants are in trans through parental or offspring testing. Population homozygote observations and functional descriptions of p.Ala222Val do not establish the required affected-proband compound-heterozygous phase observation.
For recessive disorders, detected in trans with a pathogenic variant ... This requires testing of parents (or offspring) to determine phase.
The case materials do not document an assumed de novo occurrence of NM_005957.5:c.665C>T in an affected patient, nor do they provide parental testing or a documented absence of family history. Therefore PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
The case materials contain no affected family members, meioses, familial genotypes, or phenotype-segregation observations for NM_005957.5:c.665C>T. Consequently, co-segregation cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The case evidence supplied does not provide an evaluated patient phenotype or family history for this variant. Without a documented phenotype that is highly specific for a disease with a single genetic etiology, PP4 cannot be adjudicated.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 is not assessed. gnomAD documents many homozygotes, but the available population records do not establish that specific individuals were healthy adults, and the case does not document the required inheritance model or that full penetrance is expected at an early age for the disorder being evaluated. Homozygote counts alone therefore cannot satisfy the complete BS2 definition.
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.
The case materials do not document affected relatives who lack NM_005957.5:c.665C>T, nor do they provide a family pedigree, phenotype review, or an analysis excluding phenocopies. Lack of segregation therefore cannot be assessed.
Lack of segregation in affected members of a family.
The evidence does not document NM_005957.5:c.665C>T in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern. Population homozygote counts and general functional studies do not establish cis/trans phase or a pathogenic allelic partner, so BP2 cannot be assessed.
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.
The supplied case evidence does not identify a patient with a documented alternate molecular basis for disease in whom this variant was found. The absence of such case-level information prevents adjudication of BP5.
Variant found in a case with an alternate molecular basis for disease.
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_005957.5:c.665C>T in MTHFR is a missense substitution predicted to produce NP_005948.3:p.(Ala222Val). 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 MTHFR, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
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_005957.5:c.665C>T in MTHFR is a missense substitution predicted to produce NP_005948.3:p.(Ala222Val). 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 MTHFR, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_005957.5:c.665C>T in MTHFR is a missense substitution predicted to produce NP_005948.3:p.(Ala222Val). 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 MTHFR, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
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_005957.5:c.665C>T in MTHFR is a missense substitution predicted to produce NP_005948.3:p.(Ala222Val). 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 MTHFR, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in MTHFR, mapped onto the exon structure of NM_005957.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Amish440 / 910 | 0.48105 hom |
| Admixed American28657 / 59,984 | 0.487236 hom |
| Ashkenazi Jewish13619 / 29,604 | 0.463147 hom |
| East Asian15635 / 44,872 | 0.352955 hom |
| European (non-Finnish)397733 / 1,179,858 | 0.3467492 hom |
| Remaining individuals19200 / 62,494 | 0.313108 hom |
| Middle Eastern1584 / 6,062 | 0.26233 hom |
| European (Finnish)14919 / 63,990 | 0.231788 hom |
| South Asian13560 / 91,086 | 0.151194 hom |
| African/African American8201 / 74,986 | 0.11465 hom |
| Admixed American17788 / 35,440 | 0.54654 hom |
| Ashkenazi Jewish4740 / 10,370 | 0.461089 hom |
| European (non-Finnish)43635 / 129,108 | 0.347511 hom |
| Remaining individuals2325 / 7,220 | 0.32395 hom |
| East Asian5790 / 19,944 | 0.29929 hom |
| European (Finnish)5799 / 25,116 | 0.23694 hom |
| South Asian4443 / 30,616 | 0.15389 hom |
| African/African American2714 / 24,970 | 0.11158 hom |
This variant is present in gnomAD v4.1 (AF= 0.318214; MAF= 31.82138%, 513548/1613846 alleles, homozygotes = 87723) and has highest observed frequency in the Amish population (AF= 0.483516; MAF= 48.35165%, 440/910 alleles, homozygotes = 105); grpmax FAF= 0.473111.
This variant is present in gnomAD v2.1 (AF= 0.308483; MAF= 30.84828%, 87234/282784 alleles, homozygotes = 15819) and has highest observed frequency in the Admixed American population (AF= 0.501919; MAF= 50.19187%, 17788/35440 alleles, homozygotes = 4654); grpmax FAF= 0.496463.
This variant is present in gnomAD-Canada v1.0 (AF= 0.3201935624184428, 5889/18392 alleles, homozygotes = 1086).
NM_005957.5:c.665C>T produces the missense substitution NP_005948.3:p.(Ala222Val). Under the generic rule, the missense path uses REVEL only; SpliceAI is not used for PP3/BP4 in this situation. The REVEL score is 0.842, which meets the supplied generic PP3 moderate threshold of >=0.773 but does not meet the strong threshold of >=0.932. Therefore PP3 is met at moderate strength. BayesDel has no established generic ACMG-strength calibration and is not used.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)....Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant....PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
NM_005957.5:c.665C>T is a missense variant, so BP4 must be assessed using REVEL only; the SpliceAI result cannot be substituted into the missense path. REVEL is 0.842, above the generic BP4 supporting threshold of <=0.29 and therefore in neither a BP4 range nor a benign computational range. BP4 is not met. BayesDel has no established generic ACMG-strength calibration and is not used.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)....Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant....BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
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_005957.5:c.665C>T in MTHFR is a missense substitution predicted to produce NP_005948.3:p.(Ala222Val). 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 MTHFR, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.842. BayesDel score = 0.547323.
9 paper records listed. 4 cited in the classification.
The first, 677C>T (A222V), lies within the catalytic domain and decreases enzyme activity by approximately 60% when present in the homozygous state.
Location Introduction, paragraph discussing the two common MTHFR polymorphisms
Context The paper summarizes prior functional studies of the common 677C>T variant and uses recombinant human MTHFR bacterial-expression constructs carrying the 677T/valine allele as background for testing other mutations.
Following heat treatment of those mutant cells with detectable MTHFR activity (42 cell lines), those with the CC genotype had 42 ± 11% activity remaining compared to parallel cell lysates without heat treatment, those with CT had 29 ± 14% activity remaining, and TT had 21 ± 9%.
Location Results, section ‘SNPs and thermolability’
Context Genotyping of 76 mutant MTHFR cell lines; heat-treatment thermolability assay performed on 42 mutant cell lines with detectable MTHFR activity; activity measured in cultured patient fibroblast lysates.
Of the few common variants, p.Ala222Val has been particularly well studied, and the effect of this variation in lowering protein stability [Frosst, et al., 1995] and residual enzymatic activity when found in combination with severe mutations [Sibani, et al., 2003] needs to be borne in mind.
Location Introduction, paragraph following the description of the MTHFR gene and transcript isoforms
Context Review article summarizing prior studies of common and severe MTHFR variants, including protein stability and residual enzymatic activity observations.
Using the same procedures, we identified a C to T substitution at nucleotide (nt) 677, which converts an alanine to a valine residue
Location Results, mutation identification; Table 1; Figure 2
Context Genotyping and MTHFR enzyme activity, thermolability, and plasma homocysteine measurements in 40 individuals; allele-frequency analysis in 114 unselected French Canadian chromosomes; mutagenized versus wild-type MTHFR cDNA expression in E. coli with heat-treatment assay.
Methotrexate intolerance was encountered in seven of 21 CC patients (33.3%), in six out of 25 CT patients (24%) and in nine of 15 TT patients (60%) (P = 0.03, Fisher's exact test).
Results, page 1917; Table 2
The variant classification approach described in this paper is meant to be applicable to variants in all Mendelian genes whether identified by single gene tests, multi-gene panels, exome sequencing or genome sequencing.
Introduction, final paragraph
The first, 677C→T, changes an evolutionarily conserved alanine into a valine residue, resulting in a thermolabile enzyme which can be stabilized by folate and FAD.
Introduction, page 281; Discussion, pages 285–286
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.318214; MAF= 31.82138%, 513548/1613846 alleles, homozygotes = 87723) and has highest observed frequency in the Amish population (AF= 0.483516; MAF= 48.35165%, 440/910 alleles, homozygotes = 105); grpmax FAF= 0.473111.
This variant is present in gnomAD v2.1 (AF= 0.308483; MAF= 30.84828%, 87234/282784 alleles, homozygotes = 15819) and has highest observed frequency in the Admixed American population (AF= 0.501919; MAF= 50.19187%, 17788/35440 alleles, homozygotes = 4654); grpmax FAF= 0.496463.
This variant is present in gnomAD-Canada v1.0 (AF= 0.3201935624184428, 5889/18392 alleles, homozygotes = 1086).
This variant has been reported in ClinVar as Benign (8 clinical laboratories) and as Pathogenic (3 clinical laboratories) and as Uncertain significance (3 clinical laboratories) and as Likely benign (1 clinical laboratory) and as Association (1 clinical laboratory) and as other (1 clinical laboratory) and as Likely Pathogenic (1 clinical laboratory) and as drug response by ClinPGx (expert panel). (ClinVarID = 3520)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.842. BayesDel score = 0.547323.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MTHFR, a reductase in the folate cycle, is altered in various cancers.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.