Is BMS1 p.Val150Ala (c.449T>C) pathogenic?

BMS1 p.Val150Ala (c.449T>C) is classified Uncertain significance in BMS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-14). AlphaMissense: ambiguous (0.3979); Absent from gnomAD v4.1.

How common is BMS1 p.Val150Ala (c.449T>C) in the general population?

BMS1 p.Val150Ala (c.449T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BMS1 p.Val150Ala (c.449T>C)?

AlphaMissense predicts ambiguous (score 0.3979) — an in-silico prediction, not a clinical call.

BMS1 p.Val150Ala

c.449T>C · rs1349217853 · VCV3134629

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3979 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.3979	ambiguous
REVEL	0.361	indeterminate
SaProt	LLR -6.18	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.1	GERP 1.8, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 7,350 bp · p 3.4e-05 · regional, not allelic
Overall
CADD	24.0	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

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: BMS1
Protein: p.Val150Ala
Coding: c.449T>C
MANE Select: NM_014753
dbSNP: rs1349217853
Type: single nucleotide variant
Location: chr10:42790324 (GRCh38)
Gene constraint: LOEUF 0.507 · pLI 0.50 (gnomAD)
Structure: AlphaFold pLDDT 72.04 · 3 PDB
Residue 150: 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-val150ala (accessed [today's date]).

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