Is BCAP31 c.*4C>G pathogenic?

BCAP31 c.4C>G is classified Likely benign in BCAP31 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-09-17). Absent from gnomAD v4.1; Associated with BCAP31-related disorder.

What condition is associated with BCAP31 c.*4C>G?

BCAP31 c.*4C>G is associated with BCAP31-related disorder (ClinVar).

How common is BCAP31 c.*4C>G in the general population?

BCAP31 c.*4C>G is absent from gnomAD v4.1 (gnomAD).

BCAP31 c.*4C>G

VCV3349339

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,201,408)

Conditions

BCAP31-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.27	GERP -1.7
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained
Overall
CADD	7.814	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,201,408). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BCAP31
Coding: c.*4C>G
MANE Select: NM_001256447
Type: single nucleotide variant
Location: chrX:153700933 (GRCh38)
Structure: AlphaFold pLDDT 84.74 · 3 PDB

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

Disease context

BCAP31-related disorder

Similar variants

BCAP31 p.Met1Ile Likely pathogenic ★ same condition
BCAP31 c.-44-256G>T Uncertain significance ★ same condition
BCAP31 p.Ala235Thr Uncertain significance ⚠ same condition
BCAP31 c.-12_-10del Likely benign same condition
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

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-c-star-4c-g (accessed [today's date]).

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