Is BCAP31 p.Glu245fs (c.733_736del) pathogenic?

BCAP31 p.Glu245fs (c.733736del) is classified Uncertain significance in BCAP31 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-10-01). Absent from gnomAD.

How common is BCAP31 p.Glu245fs (c.733_736del) in the general population?

BCAP31 p.Glu245fs (c.733_736del) is absent from gnomAD (gnomAD).

BCAP31 p.Glu245fs

c.733_736del · rs1603221175 · VCV807839

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (8 of 8) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP -0.86, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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
Protein: p.Glu245fs
Coding: c.733_736del
MANE Select: NM_001256447
dbSNP: rs1603221175
Type: Microsatellite
Location: chrX:153700942 (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.Glu245Lys Uncertain significance ★★ ⚠ same residue
BCAP31 p.Leu122fs Pathogenic ★★ same type
BCAP31 p.Tyr104fs Pathogenic ★ same type
BCAP31 p.Asp75del Uncertain significance ★ same type
BCAP31 p.Phe52del Uncertain significance ★ same type
BCAP31 c.478-276GCCAGGG[2] 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/bcap31-p-glu245fs (accessed [today's date]).

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