CCDC14 p.Arg16Ser
c.48G>C · rs1255624940 · VCV3138397
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00491%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.221 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -1.8, phastCons 0.015 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 46 kb · p 0.97 · regional, not allelic |
| Overall | ||
| CADD | 20.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00491%
East Asian · 2/40,710 alleles
Filtering AF
0.000814%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000305%
Overall
0.000215%
3/1,392,160 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00491% | 20,355 |
| European (non-Finnish) | 8.76e-05% | 1,141,166 |
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.Arg16Ser
- Coding
- c.48G>C
- MANE Select
- NM_001366335
- dbSNP
- rs1255624940
- Type
- single nucleotide variant
- Location
- chr3:123956778 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.45
- Residue 16
- the 'disordered' region
Similar variants
- CCDC14 p.Arg16Thr Uncertain significance ★ same residue
- CCDC14 p.Gly16Ser Uncertain significance ★ same residue
- 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
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-arg16ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown