BSND p.Lys59fs
c.174del · rs2523064807 · VCV2030162
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 4 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.3, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- BSND
- Protein
- p.Lys59fs
- Coding
- c.174del
- MANE Select
- NM_057176
- dbSNP
- rs2523064807
- Type
- Deletion
- Location
- chr1:54999357 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.80
- Residue 59
- 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.157_177+20del Pathogenic/Likely pathogenic ★★ same type
- BSND p.Gly48fs Pathogenic/Likely pathogenic ★★ same type
- BSND p.Tyr107fs Pathogenic/Likely pathogenic ★★ same type
- BSND p.Ala156fs Likely pathogenic ★ same type
- BSND p.Gln118fs Likely pathogenic ★ same type
- BSND p.Ser74fs Pathogenic ★ same type
- BSND p.Ala262fs Uncertain significance ★ same type
- BSND p.Asn265fs 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/bsnd-p-lys59fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown