CCDC141 p.Pro707Ser
c.2119C>T · rs142479179 · VCV737595
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.319%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.079 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 1.2, phastCons 1 |
| Regional constraint | o/e 1.06 | unconstrained · MANE · 216 kb · p 0.0073 · regional, not allelic |
| Overall | ||
| CADD | 19.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.319%
African / African-American · 239/75,020 alleles
Filtering AF
0.285%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.273%
Overall
0.0165%
266/1,613,846 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.319% | 314 |
| Admixed American | 0.025% | 4,000 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| East Asian | 0.00223% | 44,864 |
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.Pro707Ser
- Coding
- c.2119C>T
- MANE Select
- NM_173648
- dbSNP
- rs142479179
- Type
- single nucleotide variant
- Location
- chr2:178871513 (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-pro707ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown