BSND p.Cys54=
c.162C>T · rs942451327 · VCV1566285
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000935%, nfe)
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 0.79 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 10.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000935%
European (non-Finnish) · 11/1,176,772 alleles
Filtering AF
0.000502%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000367%
Overall
0.000755%
11/1,457,596 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.Cys54=
- Coding
- c.162C>T
- MANE Select
- NM_057176
- dbSNP
- rs942451327
- Type
- single nucleotide variant
- Location
- chr1:54999348 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.80
- Residue 54
- 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 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-cys54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown