CLP1 p.Asp269=
c.807C>T · rs140965892 · VCV1593739
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, afr)
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 1.8 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 8.809 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
African / African-American · 25/75,046 alleles
Filtering AF
0.0231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00161%
26/1,614,184 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0333% | 3,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
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
- CLP1
- Protein
- p.Asp269=
- Coding
- c.807C>T
- MANE Select
- NM_006831
- dbSNP
- rs140965892
- Type
- single nucleotide variant
- Location
- chr11:57660965 (GRCh38)
- Gene constraint
- LOEUF 0.856 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.95 · 2 PDB
Similar variants
- CLP1 p.Arg140His Pathogenic/Likely pathogenic ★★ same type
- CLP1 p.Arg116Gln Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg143Cys Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg288Cys Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg288His Uncertain significance ★★ ⚠ same type
- CLP1 p.Asn95Ser Uncertain significance ★★ ⚠ same type
- CLP1 p.Cys215Tyr Uncertain significance ★★ ⚠ same type
- CLP1 p.Glu175Lys 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/clp1-p-asp269 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown