CCDC141 p.Ala939=
c.2817G>A · rs12464157 · VCV1260713
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 22.3%, amr) — too common for a highly-penetrant pathogenic allele
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 1.8 | GERP -5.3, phastCons 0.46 |
| Overall | ||
| CADD | 3.639 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.3%
Admixed American · 13,124/58,736 alleles
Filtering AF
22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 21.9%
Overall
8.58%
137,944/1,607,508 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 22.3% | 4 |
| Middle Eastern | 8.87% | 11 |
| European (non-Finnish) | 8.86% | 11 |
| Remaining individualsnot grpmax-eligible | 8.14% | 12 |
| South Asian | 7.07% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 6.92% | 14 |
| Amishnot grpmax-eligible | 6.26% | 16 |
| East Asian | 5.62% | 18 |
| Finnishnot grpmax-eligible | 4.32% | 23 |
| African / African-American | 1.69% | 59 |
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
- CCDC141
- Protein
- p.Ala939=
- Coding
- c.2817G>A
- MANE Select
- NM_173648
- dbSNP
- rs12464157
- Type
- single nucleotide variant
- Location
- chr2:178856305 (GRCh38)
- Gene constraint
- LOEUF 1.052 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.36
Similar variants
- CCDC141 p.Ala939Thr Uncertain significance ★ same residue
- CCDC141 p.Ala1261Val Uncertain significance ★★ same type
- CCDC141 p.Ala88Thr Uncertain significance ★★ same type
- CCDC141 p.Arg1346Trp Uncertain significance ★★ same type
- CCDC141 p.Arg1463Ser Uncertain significance ★★ same type
- CCDC141 p.Arg1482Trp Uncertain significance ★★ same type
- CCDC141 p.Arg180Trp Uncertain significance ★★ same type
- CCDC141 p.Arg287Gln 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/ccdc141-p-ala939 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown