CLCNKA p.Phe362=
c.1086C>T · rs146831535 · VCV447080
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, 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 -16 | GERP -3.4 |
| Overall | ||
| CADD | 0.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
African / African-American · 1,053/74,988 alleles
Filtering AF
1.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.31%
Overall
0.0919%
1,482/1,612,294 alleles · low-frequency
exomes 803/1,460,012 · genomes 679/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.4% | 71 |
| Ashkenazi Jewishnot grpmax-eligible | 0.206% | 485 |
| Admixed American | 0.183% | 546 |
| Remaining individualsnot grpmax-eligible | 0.13% | 770 |
| Middle Eastern | 0.118% | 848 |
| European (non-Finnish) | 0.0136% | 7,374 |
| South Asian | 0.011% | 9,103 |
| East Asian | 0.00223% | 44,876 |
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
- CLCNKA
- Protein
- p.Phe362=
- Coding
- c.1086C>T
- MANE Select
- NM_004070
- dbSNP
- rs146831535
- Type
- single nucleotide variant
- Location
- chr1:16029158 (GRCh38)
- Gene constraint
- LOEUF 0.959 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.10 · 1 PDB
Similar variants
- CLCNKA p.Met227Val Uncertain significance ★★ ⚠ same type
- CLCNKA p.Ser660Leu Uncertain significance ★★ ⚠ same type
- CLCNKA p.Thr628Met Uncertain significance ★★ ⚠ same type
- CLCNKA c.100+10A>G Benign/Likely benign ★★ same type
- CLCNKA c.100+122C>T Benign ★★ same type
- CLCNKA c.101-133C>T Benign ★★ same type
- CLCNKA c.101-172C>G Benign ★★ same type
- CLCNKA c.101-267A>G Benign ★★ 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/clcnka-p-phe362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown