CCDC141 p.His770=
c.2310C>T · rs200376493 · VCV1651718
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.264%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.51 | GERP -5.8, phastCons 0.001 |
| Overall | ||
| CADD | 11.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.264%
Middle Eastern · 16/6,058 alleles
Filtering AF
0.166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.135%
Overall
0.00818%
132/1,613,528 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.264% | 379 |
| South Asian | 0.0659% | 1,517 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,471 |
| European (non-Finnish) | 0.00322% | 31,046 |
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.His770=
- Coding
- c.2310C>T
- MANE Select
- NM_173648
- dbSNP
- rs200376493
- Type
- single nucleotide variant
- Location
- chr2:178869201 (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-his770 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown