Is BCAP31 p.Thr121Ser (c.361A>T) pathogenic?

BCAP31 p.Thr121Ser (c.361A>T) is classified Likely benign in BCAP31 (ClinVar, No assertion criteria, 2 submitters). AlphaMissense: likely benign (0.1484); Very rare (popmax 0.00218%, amr).

How common is BCAP31 p.Thr121Ser (c.361A>T) in the general population?

BCAP31 p.Thr121Ser (c.361A>T) is very rare (popmax 0.00218%, amr) (gnomAD).

What do computational predictors say about BCAP31 p.Thr121Ser (c.361A>T)?

AlphaMissense predicts likely benign (score 0.1484) — an in-silico prediction, not a clinical call.

BCAP31 p.Thr121Ser

c.361A>T · rs782125326 · VCV1206221

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1484 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00218%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1484	likely benign
REVEL	0.123	moderately benign-leaning
SaProt	LLR -6.14	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.57	acceptor gain · deltas
Pangolin	Δ0.45	gain · loss 0.26 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 6.1	GERP 1.7, phastCons 1
Regional constraint	o/e 0.64	unconstrained · MANE · 22 kb · p 6.9e-07 · regional, not allelic
Overall
CADD	25.2	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 0.00218% Admixed American · 1/45,915 alleles

Filtering AF 0.00101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000798%

Overall 0.00155% 17/1,096,048 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00218%	45,915
Remaining individualsnot grpmax-eligible	0.0021%	47,520
European (non-Finnish)	0.00168%	59,628

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.Thr121Ser
Coding: c.361A>T
MANE Select: NM_001256447
dbSNP: rs782125326
Type: single nucleotide variant
Location: chrX:153704075 (GRCh38)
Structure: AlphaFold pLDDT 84.74 · 3 PDB

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

Similar variants

BCAP31 p.Arg118Cys Uncertain significance ★★ ⚠ same type
BCAP31 p.Glu245Lys Uncertain significance ★★ ⚠ same type
BCAP31 p.Gly165Arg Uncertain significance ★★ ⚠ same type
BCAP31 p.Gly239Asp Uncertain significance ★★ ⚠ same type
BCAP31 p.Ile56Val Uncertain significance ★★ ⚠ same type
BCAP31 p.Leu226Val Uncertain significance ★★ ⚠ same type
BCAP31 p.Leu40Pro Uncertain significance ★★ ⚠ same type
BCAP31 p.Lys30Arg Uncertain significance ★★ ⚠ 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/bcap31-p-thr121ser (accessed [today's date]).

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