BSND p.Val63Ile
c.187G>A · rs761711473 · VCV2187027
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0767 | likely benign |
|---|---|---|
| REVEL | 0.018 | moderately benign-leaning |
| SaProt | LLR -6.74 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.3 | GERP 0.18, phastCons 0.002 |
| Regional constraint | o/e 0.91 | unconstrained · MANE · 9,438 bp · p 0.065 · regional, not allelic |
| Overall | ||
| CADD | 3.05 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,793 |
| East Asian | 0.00223% | 44,896 |
| European (non-Finnish) | 0.00195% | 51,305 |
| Admixed American | 0.00167% | 59,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
| African / African-American | 0.00133% | 74,910 |
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.Val63Ile
- Coding
- c.187G>A
- MANE Select
- NM_057176
- dbSNP
- rs761711473
- Type
- single nucleotide variant
- Location
- chr1:55005031 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.80
- Residue 63
- a UniProt-annotated variant site (in barts4a); a UniProt-annotated variant site (in barts4a; loss of clcnka and clcnkb channel conductance); the 'regulates channel membrane trafficking and ion conductance' region
Similar variants
- BSND p.Val63= Benign/Likely benign ★★ same residue
- 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
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-val63ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown