Is BMS1 p.Val87Ala (c.260T>C) pathogenic?

BMS1 p.Val87Ala (c.260T>C) is classified Likely benign in BMS1 (ClinVar, Single submitter, 2 submitters; last evaluated 2018-11-05). AlphaMissense: likely pathogenic (0.8703); Rare (popmax 0.209%, eas).

How common is BMS1 p.Val87Ala (c.260T>C) in the general population?

BMS1 p.Val87Ala (c.260T>C) is rare (popmax 0.209%, eas) (gnomAD).

What do computational predictors say about BMS1 p.Val87Ala (c.260T>C)?

AlphaMissense predicts likely pathogenic (score 0.8703) — an in-silico prediction, not a clinical call.

BMS1 p.Val87Ala

c.260T>C · rs201298233 · VCV794146

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8703 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.209%, eas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8703	likely pathogenic
REVEL	0.462	indeterminate
SaProt	LLR -11.51	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 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 7,350 bp · p 3.4e-05 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.209% East Asian · 94/44,880 alleles

Filtering AF 0.175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.162%

Overall 0.0083% 134/1,613,946 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.209%	477
Remaining individualsnot grpmax-eligible	0.016%	6,249
Admixed American	0.01%	10,003
South Asian	0.00878%	11,384
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600
European (non-Finnish)	0.00127%	78,657

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: BMS1
Protein: p.Val87Ala
Coding: c.260T>C
MANE Select: NM_014753
dbSNP: rs201298233
Type: single nucleotide variant
Location: chr10:42785565 (GRCh38)
Gene constraint: LOEUF 0.507 · pLI 0.50 (gnomAD)
Structure: AlphaFold pLDDT 72.04 · 3 PDB
Residue 87: the bms1-type g domain; a β-strand

Full BMS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BMS1 p.Ala214Val Benign/Likely benign ★★ same type
BMS1 p.Ala500= Benign/Likely benign ★★ same type
BMS1 p.Arg237His Benign ★★ same type
BMS1 p.Arg38Trp Benign/Likely benign ★★ ⚠ same type
BMS1 p.Arg863= Benign ★★ same type
BMS1 p.Asp768Asn Benign ★★ same type
BMS1 p.Glu1278= Likely benign ★★ same type
BMS1 p.Ile942= Benign/Likely benign ★★ 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/bms1-p-val87ala (accessed [today's date]).

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