CCDC141 p.Ser426=
c.1278C>T · rs749928552 · VCV718582
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0412%, amr)
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 -4.6 | GERP -4.1 |
| Overall | ||
| CADD | 0.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0412%
Admixed American · 21/50,958 alleles
Filtering AF
0.0275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.00271%
42/1,550,316 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0412% | 2,427 |
| Remaining individualsnot grpmax-eligible | 0.00664% | 15,053 |
| South Asian | 0.00476% | 21,007 |
| African / African-American | 0.00274% | 36,469 |
| European (non-Finnish) | 0.000959% | 104,252 |
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.Ser426=
- Coding
- c.1278C>T
- MANE Select
- NM_173648
- dbSNP
- rs749928552
- Type
- single nucleotide variant
- Location
- chr2:178888656 (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-ser426 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown