KCNC1 p.Ser142=
c.426G>C · VCV4910963
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -4 | GERP -3.8 |
| Overall | ||
| CADD | 5.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KCNC1
- Protein
- p.Ser142=
- Coding
- c.426G>C
- MANE Select
- NM_001112741
- Type
- single nucleotide variant
- Location
- chr11:17736428 (GRCh38)
- Gene constraint
- LOEUF 0.363 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.51 · 10 PDB
- Residue 142
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- KCNC1 p.Ser142Leu Uncertain significance ★ ⚠ same residue
- KCNC1 p.Ala421Val Pathogenic/Likely pathogenic ★★ same type
- KCNC1 p.Arg320His Pathogenic/Likely pathogenic ★★ same type
- KCNC1 p.Thr399Met Pathogenic/Likely pathogenic ★★ same type
- KCNC1 p.Val425Met Pathogenic/Likely pathogenic ★★ same type
- KCNC1 p.Ala360Thr Uncertain significance ★★ ⚠ same type
- KCNC1 p.Ala418Ser Uncertain significance ★★ ⚠ same type
- KCNC1 p.Ala510Val 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/kcnc1-p-ser142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown