Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
FH
Final classification
VUS
FH c.364_367del · p.Lys122GlnfsTer5
FH

NM_000143.4:c.364_367del is a 4-base pair deletion in exon 3 of FH that creates a frameshift and premature termination at codon 126 (p.Lys122GlnfsTer5), predicted to undergo nonsense-mediated decay and result in complete loss of fumarate hydratase function.

Gene
FH
Transcript
NM_000143.4
HGVS · transcript:coding
NM_000143.4:c.364_367del
Consequence
N/A
GRCh38
chr1:241513613 GCCTT>G
GRCh37
chr1:241676913 GCCTT>G
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, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
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, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
FH c.364_367del

NM_000143.4:c.364_367del is a 4-base pair deletion in exon 3 of FH that creates a frameshift and premature termination at codon 126 (p.Lys122GlnfsTer5), predicted to undergo nonsense-mediated decay and result in complete loss of fumarate hydratase function.1 FH loss of function is an established disease mechanism for autosomal dominant hereditary leiomyomatosis and renal cell cancer (HLRCC), supported by extensive germline literature demonstrating that protein-truncating FH mutations cause MCUL/HLRCC through a classic two-hit tumor suppressor mechanism.2 The variant is absent from large population databases including gnomAD v2.1 and v4.1, with zero alleles observed across over 250,000 screened individuals.3 Under the generic ACMG/AMP 2015 framework, this variant meets PVS1 at very_strong strength (null variant in a gene where LoF is a known disease mechanism) and PM2 at supporting strength (absent from population databases). Per the ACMG combination rules, one very_strong criterion with one supporting criterion is most consistent with a Likely Pathogenic classification. Although the strict ACMG 2015 combination table requires two supporting criteria or one moderate criterion with PVS1 for a Pathogenic classification, the totality of evidence — a definitive null variant in a well-established tumor suppressor gene, completely absent from population databases — supports a Likely Pathogenic designation with a recommendation to consider upgrading to Pathogenic if additional evidence (e.g., patient phenotype consistent with HLRCC, segregation data, or functional confirmation) becomes available.4

PVS1 + PM2 VUS
Gene diagram · NM_000143.4 · variants mapped to exon structure
FH NM_000143.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000143.4:c.364_367del is a 4-base pair deletion in exon 3 of 10 that creates a frameshift and premature termination codon (p.Lys122GlnfsTer5) at amino acid 126 of 510, predicted to trigger nonsense-mediated decay. FH loss of function is an established disease mechanism for hereditary leiomyomatosis and renal cell cancer (HLRCC), supported by extensive germline literature. Under ClinGen SVI PVS1 recommendations (PMC6185798), a frameshift variant predicted to undergo NMD in a gene where LoF is the established mechanism qualifies for PVS1 at full strength.
4-bp frameshift deletion in exon 3/10premature stop at codon 126NMD predicted (truncation >75% of protein
PM2 supporting Pathogenic
NM_000143.4:c.364_367del is absent from gnomAD v2.1 (exomes) and gnomAD v4.1 (exomes/genomes), representing a total of over 250,000 alleles screened without observation. Under generic ACMG/AMP 2015 rules for non-VCEP genes, absence from large population databases at an allele frequency below 0.1% qualifies for PM2 at supporting strength.
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)
Assessed · not applied
Pathogenic
PS2 No de novo data were identified for this variant in the reviewed literature or ClinVar submissions.
PS3 No variant-specific functional data were identified for NM_000143.4:c.364_367del.
PS4 No variant-specific prevalence or case-control data were identified.
PM1 The variant is not located in a statistically significant mutational hotspot (cancerhotspots.org negative).
PM6 No de novo observation was identified for this variant in the reviewed literature or databases.
PP1 No segregation data are available for this variant.
PP3 SpliceAI predicts no significant splice impact (max delta score 0.02).
PP4 No patient-specific phenotype data are available for this variant assessment.
PP5 This variant is absent from ClinVar.
Benign
BA1 The variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0.
BS1 The variant is absent from gnomAD v2.1 and v4.1.
BS2 No data are available regarding observation of this variant in healthy adult individuals.
BS3 No functional studies demonstrate a benign effect for this variant.
BS4 No segregation data are available.
BP2 No data are available regarding observation of this variant in trans with a known pathogenic variant.
BP4 SpliceAI predicts no significant splice impact (max delta 0.02), but this is a protein-truncating frameshift variant whose pathogenicity is mediated at the protein level, not through splicing.
BP5 No data are available suggesting an alternative molecular basis for disease in a case where this variant was observed.
BP6 This variant is absent from ClinVar.
N/A · 8 PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
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. COSMIC could not be reviewed because the browser session was redirected to the login page before search results were available.
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 2 further PMIDs triaged but not cited — see Sources & References.
Germline mutations in FH predispose to dominantly inherited uterine fibroids, skin leiomyomata and papillary renal cell cancer.
Searched
c.364_367del364del367delK122QfsLys122Glnfs122fsexon 3codon 122
Found
Describes the discovery that germline FH mutations cause multiple cutaneous and uterine leiomyomatosis and papillary renal cell cancer. Reports 25 mutations (truncating, missense, in-frame deletion) in 42 probands, demonstrating that FH acts as a tumor suppressor with loss of the wild-type allele in tumors and reduced fumarate hydratase enzyme activity in affected individuals. NM_000143.4:c.364_367del was not among the reported mutations.
Variant
◇ Residue / gene-level — variant not named
Applied to
PVS1 supports · met
Why
Variant not identified in this paper. Used as gene-level evidence supporting FH loss-of-function mechanism for PVS1 eligibility, but not cited as variant-specific evidence.
We found mutations in FH in 25 of the 42 probands analyzed (Table 1), including protein-truncating mutations, the two large germline deletions, missense changes and an in-frame deletion.
Location Table 1 lists all 24 specific mutations (none match); Results section describes mutation spectrum and functional enzyme assays in lymphoblastoid cells and tumors.  ·  Context Lymphoblastoid cell line fumarate hydratase activity assays; tumor LOH analysis by microsatellite markers  ·  full text
Genetic and functional analyses of FH mutations in multiple cutaneous and uterine leiomyomatosis, hereditary leiomyomatosis and renal cancer, and fumarate hydratase deficiency.
Searched
c.364_367del364delK122QfsLys122GlnfsK122122fsexon 3 frameshiftcodon 122
Found
Reports additional FH mutations in MCUL and fumarate hydratase deficiency patients. Characterizes 20 distinct germline mutations in 35 of 46 MCUL probands, maps them onto the FH crystal structure, and demonstrates that protein-truncating FH mutations are functionally null alleles. NM_000143.4:c.364_367del was not among the reported mutations.
Variant
◇ Residue / gene-level — variant not named
Applied to
PVS1 supports · met
Why
Variant not identified in this paper. Used as gene-level evidence that FH truncating mutations are functionally null, supporting PVS1 strength assignment, but not cited as variant-specific evidence.
Protein-truncating FH mutations are functionally null alleles.
Location Table 1 lists all 20 mutations (none match); Results section 'Mutations in MCUL patients' describes mutation types and functional characterization.  ·  Context Lymphoblastoid cell line fumarase activity assays; western blotting for protein stability; structural modeling onto E. coli fumarase C crystal structure  ·  full text
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
12772087 ↗ Mutations in the fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. ONCOKB
15937070 ↗ Novel mutations in FH and expansion of the spectrum of phenotypes expressed in families with hereditary leiomyomatosis and renal cell cancer. ONCOKB