KCNC3 p.Asp63fs
c.186_192del · VCV3779779
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
spinocerebellar ataxia type 13
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 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -3.5, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | (CGG)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- KCNC3
- Protein
- p.Asp63fs
- Coding
- c.186_192del
- MANE Select
- NM_004977
- Type
- Deletion
- Location
- chr19:50328891 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI 0.30 (gnomAD)
- Structure
- AlphaFold pLDDT 66.01
- Residue 63
- the 'disordered' region; the 'important for normal n-type inactivation' region; a UniProt-annotated variant site (in)
Disease context
spinocerebellar ataxia type 13 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Spinocerebellar ataxia type 13 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult
Similar variants
- KCNC3 p.Asp63Gly Benign/Likely benign ★★ same residue
- KCNC3 p.Ser4fs Pathogenic ★ same condition
- KCNC3 p.Gly606_Val607insTer Uncertain significance ★ same condition
- KCNC3 p.Arg420His Pathogenic ★★ same condition
- KCNC3 p.Arg423His Pathogenic ★★ same condition
- KCNC3 p.Ala749Thr Uncertain significance ★★ ⚠ same condition
- KCNC3 p.Gly231Ser Uncertain significance ★★ ⚠ same condition
- KCNC3 p.Gly251Ser Uncertain significance ★★ ⚠ same condition
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/kcnc3-p-asp63fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown