BSND p.Asp169=
c.507C>T · rs749127391 · VCV1143353
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 -9.3 | GERP -2.8 |
| Overall | ||
| CADD | 0.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,964 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00682%
Overall
0.00217%
35/1,612,332 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,996 |
| East Asian | 0.00446% | 22,420 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,562 |
| South Asian | 0.00329% | 30,351 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,204 |
| European (non-Finnish) | 0.00144% | 69,335 |
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
- BSND
- Protein
- p.Asp169=
- Coding
- c.507C>T
- MANE Select
- NM_057176
- dbSNP
- rs749127391
- Type
- single nucleotide variant
- Location
- chr1:55007231 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.80
- Residue 169
- a UniProt-annotated variant site (in barts4a); a UniProt-annotated variant site (in barts4a; loss of clcnka and clcnkb channel conductance); a UniProt-annotated variant site (in barts4a; abolishes the preferential sorting at the basolateral membrane domain; no effect on ion conductance); the 'disordered' region
Similar variants
- BSND c.178-2A>C Likely pathogenic ★★ same type
- BSND c.272+1G>T Pathogenic/Likely pathogenic ★★ same type
- BSND p.Arg8Trp Pathogenic/Likely pathogenic ★★ same type
- BSND p.Gln95Ter Pathogenic/Likely pathogenic ★★ same type
- BSND p.Glu148Ter Pathogenic/Likely pathogenic ★★ same type
- BSND p.Glu4Ter Pathogenic ★★ same type
- BSND p.Glu88Ter Pathogenic/Likely pathogenic ★★ same type
- BSND p.Gly10Ser Pathogenic/Likely pathogenic ★★ ⚠ 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/bsnd-p-asp169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown