CCDC13 p.Ala129=
c.387C>T · VCV3828128
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -4 |
| Overall | ||
| CADD | 7.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0988%
South Asian · 90/91,074 alleles
Filtering AF
0.0823%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0761%
Overall
0.0126%
204/1,613,694 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0988% | 1,012 |
| Middle Eastern | 0.0164% | 6,084 |
| East Asian | 0.0156% | 6,412 |
| Admixed American | 0.0117% | 8,568 |
| European (non-Finnish) | 0.0078% | 12,826 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,618 |
| African / African-American | 0.00401% | 24,942 |
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
- CCDC13
- Protein
- p.Ala129=
- Coding
- c.387C>T
- MANE Select
- NM_144719
- Type
- single nucleotide variant
- Location
- chr3:42752701 (GRCh38)
- Gene constraint
- LOEUF 0.906 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.77
Similar variants
- CCDC13 p.Ala129Thr Uncertain significance ★ ⚠ same residue
- CCDC13 p.Glu565Lys Uncertain significance ★★ ⚠ same type
- CCDC13 p.Ala175Thr Uncertain significance ★ ⚠ same type
- CCDC13 p.Ala187Thr Uncertain significance ★ ⚠ same type
- CCDC13 p.Ala332Gly Uncertain significance ★ ⚠ same type
- CCDC13 p.Ala3Val Uncertain significance ★ ⚠ same type
- CCDC13 p.Ala517Val Uncertain significance ★ ⚠ same type
- CCDC13 p.Ala544Thr 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/ccdc13-p-ala129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown