CLCNKB p.Ser159=
c.477C>T · rs1400748522 · VCV2985037
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 0.25 | GERP 0.17, phastCons 0.99 |
| Overall | ||
| CADD | 6.984 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,012 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000137%
2/1,461,670 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
- CLCNKB
- Protein
- p.Ser159=
- Coding
- c.477C>T
- MANE Select
- NM_000085
- dbSNP
- rs1400748522
- Type
- single nucleotide variant
- Location
- chr1:16048023 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.16
Similar variants
- CLCNKB c.968+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLCNKB p.Ala204Thr Pathogenic/Likely pathogenic ★★ same type
- CLCNKB p.Ala77Pro Pathogenic/Likely pathogenic ★★ same type
- CLCNKB p.Arg304Ter Pathogenic/Likely pathogenic ★★ same type
- CLCNKB p.Arg438His Pathogenic ★★ same type
- CLCNKB p.Arg595Ter Pathogenic ★★ same type
- CLCNKB p.Arg76Ter Pathogenic ★★ same type
- CLCNKB p.Glu225Ter 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/clcnkb-p-ser159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown