Is F12 p.Ser541Ala (c.1621T>G) pathogenic?

F12 p.Ser541Ala (c.1621T>G) is classified Uncertain significance in F12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). AlphaMissense: likely benign (0.0616); Very rare (popmax 8.47e-05%, nfe).

How common is F12 p.Ser541Ala (c.1621T>G) in the general population?

F12 p.Ser541Ala (c.1621T>G) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about F12 p.Ser541Ala (c.1621T>G)?

AlphaMissense predicts likely benign (score 0.0616) — an in-silico prediction, not a clinical call.

F12 p.Ser541Ala

c.1621T>G · rs752613141 · VCV2656115

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0616 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0616	likely benign
REVEL	0.092	moderately benign-leaning
SaProt	LLR -6.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.19	GERP -4.6
Regional constraint	o/e 0.97	unconstrained · MANE · 7,232 bp · p 0.39 · regional, not allelic
Overall
CADD	1.456	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 8.47e-05% European (non-Finnish) · 1/1,179,966 alleles

Overall 6.85e-05% 1/1,460,868 alleles · very rare

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: F12
Protein: p.Ser541Ala
Coding: c.1621T>G
MANE Select: NM_000505
dbSNP: rs752613141
Type: single nucleotide variant
Location: chr5:177402609 (GRCh38)
Gene constraint: LOEUF 1.286 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.47 · 17 PDB
Residue 541: an α-helix; a disulfide bond; the peptidase s1 domain

Full F12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

F12 p.Glu193Ter Pathogenic/Likely pathogenic ★★ same type
F12 p.Thr328Lys Pathogenic ★★ ⚠ same type
F12 c.57+4A>G Uncertain significance ★★ same type
F12 p.Ala452Thr Uncertain significance ★★ ⚠ same type
F12 p.Arg55Trp Uncertain significance ★★ ⚠ same type
F12 p.Asp283= Uncertain significance ★★ same type
F12 p.Glu288Lys Uncertain significance ★★ same type
F12 p.Gly360Val Uncertain significance ★★ ⚠ same type

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/f12-p-ser541ala (accessed [today's date]).

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