CCDC14 p.Pro780Ser
c.2338C>T · rs367677491 · VCV2385066
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0657%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -3.4, phastCons 0.97 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 46 kb · p 0.97 · regional, not allelic |
| Overall | ||
| CADD | 5.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0657%
Middle Eastern · 4/6,084 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.0031%
50/1,613,762 alleles · ultra-rare
exomes 48/1,461,552 · genomes 2/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0657% | 1,521 |
| African / African-American | 0.00801% | 12,486 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,614 |
| Admixed American | 0.00333% | 29,990 |
| European (non-Finnish) | 0.00271% | 36,870 |
| East Asian | 0.00223% | 44,904 |
| South Asian | 0.0011% | 91,068 |
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.Pro780Ser
- Coding
- c.2338C>T
- MANE Select
- NM_001366335
- dbSNP
- rs367677491
- Type
- single nucleotide variant
- Location
- chr3:123915159 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.45
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-pro780ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown