Is FH p.Ser35Trp (c.104C>G) pathogenic?

FH p.Ser35Trp (c.104C>G) is classified Uncertain significance in FH (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-07-29). AlphaMissense: likely benign (0.1852); Very rare (popmax 0.00137%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with FH p.Ser35Trp (c.104C>G)?

FH p.Ser35Trp (c.104C>G) is associated with hereditary neoplastic syndrome, fumaric aciduria (ClinVar).

How common is FH p.Ser35Trp (c.104C>G) in the general population?

FH p.Ser35Trp (c.104C>G) is very rare (popmax 0.00137%, afr) (gnomAD).

What do computational predictors say about FH p.Ser35Trp (c.104C>G)?

AlphaMissense predicts likely benign (score 0.1852) — an in-silico prediction, not a clinical call.

FH p.Ser35Trp

c.104C>G · rs942065027 · VCV822075

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.1852 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00137%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1852	likely benign
REVEL	0.354	indeterminate
SaProt	LLR -8.97	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.37	GERP -2, phastCons 0.003
Regional constraint	o/e 1.12	unconstrained · MANE · 6,014 bp · p 0.17 · regional, not allelic
Overall
CADD	16.12	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00137% African / African-American · 1/72,934 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000194% 3/1,547,688 alleles · very rare exomes 2/1,395,454 · genomes 1/152,234 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00137%	72,934
European (non-Finnish)	0.000174%	573,230

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: FH
Protein: p.Ser35Trp
Coding: c.104C>G
MANE Select: NM_000143
dbSNP: rs942065027
Type: single nucleotide variant
Location: chr1:241519619 (GRCh38)
Gene constraint: LOEUF 0.599 · pLI 0.27 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.92 · 8 PDB

Full FH gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: fumaric aciduria

Similar variants

FH p.Ser35Leu Uncertain significance ★★ ⚠ same residue
FH p.Ser35= Benign/Likely benign ★★ same residue
FH p.Ser35Pro Uncertain significance ★ ⚠ same residue
FH c.1108+1G>T Pathogenic/Likely pathogenic ★★ same condition
FH c.1236+1G>A Pathogenic/Likely pathogenic ★★ same condition
FH c.1236+1G>C Pathogenic ★★ same condition
FH c.1236+2T>G Pathogenic ★★ same condition
FH c.1237-1G>T Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/fh-p-ser35trp (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown