Is BMS1 p.Arg55Gly (c.163C>G) pathogenic?

BMS1 p.Arg55Gly (c.163C>G) is classified Uncertain significance in BMS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-16). AlphaMissense: likely pathogenic (0.8755); Rare (popmax 0.149%, mid).

How common is BMS1 p.Arg55Gly (c.163C>G) in the general population?

BMS1 p.Arg55Gly (c.163C>G) is rare (popmax 0.149%, mid) (gnomAD).

What do computational predictors say about BMS1 p.Arg55Gly (c.163C>G)?

AlphaMissense predicts likely pathogenic (score 0.8755) — an in-silico prediction, not a clinical call.

BMS1 p.Arg55Gly

c.163C>G · VCV3992245

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8755 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.149%, mid)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8755	likely pathogenic
REVEL	0.168	moderately benign-leaning
SaProt	LLR -14.45	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 0.54, phastCons 0.93
Regional constraint	o/e 0.77	unconstrained · MANE · 7,350 bp · p 3.4e-05 · regional, not allelic
Overall
CADD	22.2	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 0.149% Middle Eastern · 9/6,060 alleles

Filtering AF 0.0774% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0578%

Overall 0.00267% 43/1,611,848 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.149%	673
Remaining individualsnot grpmax-eligible	0.00802%	12,471
Admixed American	0.00672%	14,891
African / African-American	0.00535%	18,691
South Asian	0.00331%	30,193
European (non-Finnish)	0.00153%	65,511

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.Arg55Gly
Coding: c.163C>G
MANE Select: NM_014753
Type: single nucleotide variant
Location: chr10:42784557 (GRCh38)
Gene constraint: LOEUF 0.507 · pLI 0.50 (gnomAD)
Structure: AlphaFold pLDDT 72.04 · 3 PDB
Residue 55: an α-helix

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-arg55gly (accessed [today's date]).

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