CCDC141 p.Val487=
c.1461T>C · rs201327469 · VCV1630472
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.62%, 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 -12 | GERP -5.1 |
| Overall | ||
| CADD | 0.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.62%
South Asian · 1,177/72,492 alleles
Filtering AF
1.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.52%
Overall
0.202%
2,987/1,476,028 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.62% | 62 |
| Ashkenazi Jewishnot grpmax-eligible | 0.665% | 150 |
| Middle Eastern | 0.405% | 247 |
| Remaining individualsnot grpmax-eligible | 0.291% | 344 |
| European (non-Finnish) | 0.124% | 807 |
| Admixed American | 0.122% | 819 |
| African / African-American | 0.0233% | 4,295 |
| Finnishnot grpmax-eligible | 0.0141% | 7,096 |
| East Asian | 0.00531% | 18,848 |
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.Val487=
- Coding
- c.1461T>C
- MANE Select
- NM_173648
- dbSNP
- rs201327469
- Type
- single nucleotide variant
- Location
- chr2:178886818 (GRCh38)
- Gene constraint
- LOEUF 1.052 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.36
Similar variants
- 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
- CCDC141 p.Arg468Gln 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-val487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown