CCDC14 p.Cys63Ser
c.187T>A · VCV3263873
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000785%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.722 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>G here scores Δ0.26 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 46 kb · p 0.97 · regional, not allelic |
| Overall | ||
| CADD | 24.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000785%
European (non-Finnish) · 9/1,145,852 alleles
Filtering AF
0.00037%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000268%
Overall
0.000645%
9/1,396,086 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
- CCDC14
- Protein
- p.Cys63Ser
- Coding
- c.187T>A
- MANE Select
- NM_001366335
- Type
- single nucleotide variant
- Location
- chr3:123956088 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.45
- Residue 63
- the 'disordered' region
Similar variants
- CCDC14 c.38G>A Uncertain significance ★ same type
- CCDC14 c.-20C>T Uncertain significance ★ same type
- CCDC14 c.-30T>C Uncertain significance ★ same type
- CCDC14 c.-32C>T Uncertain significance ★ same type
- CCDC14 c.-33C>T Uncertain significance ★ same type
- CCDC14 c.-5G>A Uncertain significance ★ same type
- CCDC14 p.Ala636Pro Uncertain significance ★ same type
- CCDC14 p.Ala636Val 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/ccdc14-p-cys63ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown