CCDC141 p.Ala141Val
c.422C>T · rs10497529 · VCV1554138
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.89%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.242 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.5, phastCons 1 |
| Regional constraint | o/e 1.06 | unconstrained · MANE · 216 kb · p 0.0073 · regional, not allelic |
| Overall | ||
| CADD | 27.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.89%
Admixed American · 2,396/48,988 alleles
Filtering AF
4.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.66%
Overall
3%
43,324/1,443,594 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.89% | 20 |
| European (non-Finnish) | 3.3% | 30 |
| Ashkenazi Jewishnot grpmax-eligible | 3.17% | 32 |
| Remaining individualsnot grpmax-eligible | 2.98% | 34 |
| Middle Eastern | 2.5% | 40 |
| South Asian | 2.29% | 44 |
| Finnishnot grpmax-eligible | 1.88% | 53 |
| Amishnot grpmax-eligible | 1.21% | 83 |
| African / African-American | 0.659% | 152 |
| East Asian | 0.0151% | 6,621 |
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.Ala141Val
- Coding
- c.422C>T
- MANE Select
- NM_173648
- dbSNP
- rs10497529
- Type
- single nucleotide variant
- Location
- chr2:178975161 (GRCh38)
- Gene constraint
- LOEUF 1.052 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.36
Similar variants
- CCDC141 p.Ala141Pro 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-ala141val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown