BSND p.Lys290=
c.870G>A · rs887915316 · VCV1097439
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, 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 3.6 | GERP 0.44, phastCons 1 |
| Overall | ||
| CADD | 4.287 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,928 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.00131%
2/152,218 alleles · very rare
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.Lys290=
- Coding
- c.870G>A
- MANE Select
- NM_057176
- dbSNP
- rs887915316
- Type
- single nucleotide variant
- Location
- chr1:55008535 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.80
- Residue 290
- 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 p.Lys290Glu Uncertain significance ★★ ⚠ 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-lys290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown