Starting
Initialising…
0%
FH
Final classification
Pathogenic
FH c.301C>T · p.Arg101Ter
FH

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).

Gene
FH
Transcript
NM_000143.4
HGVS · transcript:coding
NM_000143.4:c.301C>T
Consequence
N/A
GRCh38
chr1:241513680 G>A
GRCh37
chr1:241676980 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PS3 supporting, PM2 moderate, PP5 supporting; combination = 1 very strong + 1 moderate + 2 supporting, which maps to Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PS3 supporting, PM2 moderate, PP5 supporting; combination = 1 very strong + 1 moderate + 2 supporting, which maps to Pathogenic.
Classification rationale
PVS1PS3PM2PP5 Pathogenic
FH c.301C>T

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).1 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.2 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.3 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.4 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.5 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).6 Applying the ACMG/AMP 2015 combination rules: 1 Very Strong (PVS1) + 1 Moderate (PM2) + 2 Supporting (PS3, PP5) satisfies the threshold for Pathogenic classification.7

PVS1 + PS3 + PM2 + PP5 Pathogenic
Gene diagram · NM_000143.4 · variants mapped to exon structure
FH NM_000143.4
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 7.4354e-06; MAF= 0.00074%, 12/1613900 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.01699e-05; MAF= 0.00102%, 12/1179948 alleles, homozygotes = 0); grpmax FAF= 5.42e-06.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00074% · 12 / 1,613,900
      0 hom · FAF 0.00054%
      European (non-Finnish)
      12 / 1,179,948
      0.001%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (14 clinical laboratories). (ClinVarID = 16232)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.486496.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
      Genetic and functional analyses of FH mutations in multiple cutaneous and uterine leiomyomatosis, hereditary leiomyomatosis and renal cancer, and fumarate hydratase deficiency.
      Found
      abstract: 'Protein-truncating FH mutations are functionally null alleles' PMID:16597677: FH enzyme activity significantly reduced in HLRCC lymphoblastoid and fibroblast cell lines PMID:21398687: 32 FH mutations demonstrated as deleterious by FH enzymatic activity reduction OncoKB: Likely Loss-of-function Likely Oncogenic for R101*
      Applied to
      PS3 supports · met
      Fumarate hydratase enzyme activity in lymphoblastoid cells and fibroblasts of individuals in families with hereditary leiomyomatosis and renal cell cancer.
      Found
      abstract: 'Protein-truncating FH mutations are functionally null alleles' PMID:16597677: FH enzyme activity significantly reduced in HLRCC lymphoblastoid and fibroblast cell lines PMID:21398687: 32 FH mutations demonstrated as deleterious by FH enzymatic activity reduction OncoKB: Likely Loss-of-function Likely Oncogenic for R101*
      Applied to
      PS3 supports · met
      Novel FH mutations in families with hereditary leiomyomatosis and renal cell cancer (HLRCC) and patients with isolated type 2 papillary renal cell carcinoma.
      Found
      abstract: 'Protein-truncating FH mutations are functionally null alleles' PMID:16597677: FH enzyme activity significantly reduced in HLRCC lymphoblastoid and fibroblast cell lines PMID:21398687: 32 FH mutations demonstrated as deleterious by FH enzymatic activity reduction OncoKB: Likely Loss-of-function Likely Oncogenic for R101*
      Applied to
      PS3 supports · met
      PMID 41496563
      Found
      Nonsense mutation c.301C>T creates premature stop codon p.Arg101Ter (R101*) in exon 3/10 FH loss-of-function is an established disease mechanism for HLRCC (autosomal dominant) Germline pathogenic FH variants identified in 35.7% of FH-deficient uterine leiomyomas truncating mutations significantly more prevalent in hereditary cases (PMID:41496563) NM_000143.4 is the MANE Select transcript NMD is predicted (PTC at codon 101 well upstream of the last exon-exon junction)
      Applied to
      PVS1 supports · met
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      11865300 ↗ Germline mutations in FH predispose to dominantly inherited uterine fibroids, skin leiomyomata and papillary renal cell cancer. ONCOKB
      15937070 ↗ Novel mutations in FH and expansion of the spectrum of phenotypes expressed in families with hereditary leiomyomatosis and renal cell cancer. ONCOKB
      12772087 ↗ Mutations in the fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. ONCOKB
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR