Is FH p.Arg421Ser (c.1263G>C) pathogenic?

FH p.Arg421Ser (c.1263G>C) is classified Uncertain significance in FH (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-11). AlphaMissense: likely pathogenic (0.6183); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with FH p.Arg421Ser (c.1263G>C)?

FH p.Arg421Ser (c.1263G>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is FH p.Arg421Ser (c.1263G>C) in the general population?

FH p.Arg421Ser (c.1263G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FH p.Arg421Ser (c.1263G>C)?

AlphaMissense predicts likely pathogenic (score 0.6183) — an in-silico prediction, not a clinical call.

FH p.Arg421Ser

c.1263G>C · rs777409218 · VCV1493490

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6183 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.6183	likely pathogenic
REVEL	0.621	indeterminate
SaProt	LLR -11.68	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.14	GERP -3.8, phastCons 0.51
Regional constraint	o/e 0.75	unconstrained · MANE · 16 kb · p 7.5e-09 · regional, not allelic
Overall
CADD	21.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FH
Protein: p.Arg421Ser
Coding: c.1263G>C
MANE Select: NM_000143
dbSNP: rs777409218
Type: single nucleotide variant
Location: chr1:241500564 (GRCh38)
Gene constraint: LOEUF 0.599 · pLI 0.27 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.92 · 8 PDB
Residue 421: an α-helix

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

Similar variants

FH p.Arg421Met Uncertain significance ★★ ⚠ same residue
FH p.Arg421Gly Uncertain significance ★ ⚠ same residue
FH p.Arg421Thr 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-arg421ser (accessed [today's date]).

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