Is BCAP31 p.Lys30Arg (c.89A>G) pathogenic?

BCAP31 p.Lys30Arg (c.89A>G) is classified Uncertain significance in BCAP31 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-20). AlphaMissense: likely benign (0.0792); Very rare (popmax 0.00335%, nfe); Associated with Inborn genetic diseases.

What condition is associated with BCAP31 p.Lys30Arg (c.89A>G)?

BCAP31 p.Lys30Arg (c.89A>G) is associated with Inborn genetic diseases (ClinVar).

How common is BCAP31 p.Lys30Arg (c.89A>G) in the general population?

BCAP31 p.Lys30Arg (c.89A>G) is very rare (popmax 0.00335%, nfe) (gnomAD).

What do computational predictors say about BCAP31 p.Lys30Arg (c.89A>G)?

AlphaMissense predicts likely benign (score 0.0792) — an in-silico prediction, not a clinical call.

BCAP31 p.Lys30Arg

c.89A>G · rs144781058 · VCV2904327

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0792 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00335%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0792	likely benign
REVEL	0.268	benign-leaning
SaProt	LLR -5.25	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.27	loss · gain 0.01 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 4.2	GERP 0.78, phastCons 1
Regional constraint	o/e 0.64	unconstrained · MANE · 22 kb · p 6.9e-07 · regional, not allelic
Overall
CADD	17.52	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 0.00335% European (non-Finnish) · 30/894,833 alleles

Filtering AF 0.00238% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00206%

Overall 0.00282% 31/1,097,414 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00335%	29,828
Remaining individualsnot grpmax-eligible	0.0021%	47,590

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.Lys30Arg
Coding: c.89A>G
MANE Select: NM_001256447
dbSNP: rs144781058
Type: single nucleotide variant
Location: chrX:153723156 (GRCh38)
Structure: AlphaFold pLDDT 84.74 · 3 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCAP31 p.Glu245Lys Uncertain significance ★★ ⚠ same condition
BCAP31 p.Gly165Arg Uncertain significance ★★ ⚠ same condition
BCAP31 p.Ile56Val Uncertain significance ★★ ⚠ same condition
BCAP31 p.Leu226Val Uncertain significance ★★ ⚠ same condition
BCAP31 p.Ter247Gln Likely pathogenic ★ same condition
BCAP31 c.-44-276A>G Uncertain significance ★ same condition
BCAP31 c.-44-288G>T Uncertain significance ★ same condition
BCAP31 c.-44-297A>T Uncertain significance ★ same condition

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-lys30arg (accessed [today's date]).

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