CEP63 p.Trp43Ter
c.129G>A · rs1164567042 · VCV35517
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Seckel syndrome 6
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- CEP63
- Protein
- p.Trp43Ter
- Coding
- c.129G>A
- MANE Select
- NM_001353108
- dbSNP
- rs1164567042
- Type
- single nucleotide variant
- Location
- chr3:134507193 (GRCh38)
- Gene constraint
- LOEUF 1.127 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.95 · 4 PDB
Similar variants
- CEP63 c.1067+2T>C Likely pathogenic ★★ same condition
- CEP63 c.790-2A>G Likely pathogenic ★★ same condition
- CEP63 p.Arg312Gln Uncertain significance ★★ ⚠ same condition
- CEP63 p.Asn223Ser Uncertain significance ★★ ⚠ same condition
- CEP63 p.Lys553Glu Uncertain significance ★★ ⚠ same condition
- CEP63 p.Pro658His Uncertain significance ★★ ⚠ same condition
- CEP63 c.1330-16A>G Benign/Likely benign ★★ same condition
- CEP63 c.790-1G>A Likely pathogenic ★ 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/cep63-p-trp43ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown