Is FH p.Pro63Thr (c.187C>A) pathogenic?

FH p.Pro63Thr (c.187C>A) is classified Uncertain significance in FH (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-03-04). AlphaMissense: likely pathogenic (0.6378); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with FH p.Pro63Thr (c.187C>A)?

FH p.Pro63Thr (c.187C>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is FH p.Pro63Thr (c.187C>A) in the general population?

FH p.Pro63Thr (c.187C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FH p.Pro63Thr (c.187C>A)?

AlphaMissense predicts likely pathogenic (score 0.6378) — an in-silico prediction, not a clinical call.

FH p.Pro63Thr

c.187C>A · rs1573888488 · VCV1326115

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6378 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.6378	likely pathogenic
REVEL	0.951	strongly pathogenic-leaning
SaProt	LLR -13.14	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 6,014 bp · p 0.17 · regional, not allelic
Overall
CADD	26.0	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.Pro63Thr
Coding: c.187C>A
MANE Select: NM_000143
dbSNP: rs1573888488
Type: single nucleotide variant
Location: chr1:241517262 (GRCh38)
Gene constraint: LOEUF 0.599 · pLI 0.27 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.92 · 8 PDB
Residue 63: a β-strand

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.Pro63Ser Uncertain significance ★★ ⚠ same residue
FH p.Pro63Leu Uncertain significance ★ ⚠ same residue
FH p.Pro63= Likely benign ★ 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-pro63thr (accessed [today's date]).

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