BCAP31 p.Asp164=
c.492C>T · VCV4699851
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.014%, afr)
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 -0.52 | GERP -3.1 |
| Overall | ||
| CADD | 0.504 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.014%
African / African-American · 8/57,242 alleles
Filtering AF
0.00689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00502%
Overall
0.00116%
14/1,208,117 alleles · ultra-rare
exomes 9/1,095,725 · genomes 5/112,392 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.014% | 7,155 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,468 |
| South Asian | 0.00176% | 56,828 |
| European (non-Finnish) | 0.000447% | 223,757 |
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.Asp164=
- Coding
- c.492C>T
- MANE Select
- NM_001256447
- Type
- single nucleotide variant
- Location
- chrX:153703044 (GRCh38)
- Structure
- AlphaFold pLDDT 84.74 · 3 PDB
- Residue 164
- a functional site (cleavage; by caspase-8)
Similar variants
- BCAP31 p.Asp164Glu Uncertain significance ★ ⚠ same residue
- 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
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-asp164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown