Is BCAP31 p.Arg213Trp (c.637C>T) pathogenic?

BCAP31 p.Arg213Trp (c.637C>T) is classified Uncertain significance in BCAP31 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-16). AlphaMissense: likely benign (0.1776); Ultra-rare (popmax 0.0231%, mid).

How common is BCAP31 p.Arg213Trp (c.637C>T) in the general population?

BCAP31 p.Arg213Trp (c.637C>T) is ultra-rare (popmax 0.0231%, mid) (gnomAD).

What do computational predictors say about BCAP31 p.Arg213Trp (c.637C>T)?

AlphaMissense predicts likely benign (score 0.1776) — an in-silico prediction, not a clinical call.

BCAP31 p.Arg213Trp

c.637C>T · rs372317882 · VCV2994994

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1776 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0231%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1776	likely benign
REVEL	0.303	indeterminate
SaProt	LLR -12.64	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP -2.4, phastCons 1
Regional constraint	o/e 0.64	unconstrained · MANE · 22 kb · p 6.9e-07 · regional, not allelic
Overall
CADD	25.6	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 0.0231% Middle Eastern · 1/4,336 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00271%

Overall 0.00124% 15/1,209,119 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0231%	4,336
Admixed American	0.0109%	9,153
European (non-Finnish)	0.00101%	99,347

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: BCAP31
Protein: p.Arg213Trp
Coding: c.637C>T
MANE Select: NM_001256447
dbSNP: rs372317882
Type: single nucleotide variant
Location: chrX:153702072 (GRCh38)
Structure: AlphaFold pLDDT 84.74 · 3 PDB
Residue 213: an α-helix

Full BCAP31 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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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/bcap31-p-arg213trp (accessed [today's date]).

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