CLP1 p.Pro271=
c.813C>T · rs781569229 · VCV1570147
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, mid)
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 -0.46 | GERP -5.1, phastCons 0.19 |
| Overall | ||
| CADD | 4.068 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,084 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00248%
40/1,614,088 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,217 |
| Admixed American | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,830 |
| European (non-Finnish) | 0.00212% | 47,202 |
| South Asian | 0.0011% | 91,084 |
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.Pro271=
- Coding
- c.813C>T
- MANE Select
- NM_006831
- dbSNP
- rs781569229
- Type
- single nucleotide variant
- Location
- chr11:57660971 (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-pro271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown