CASP7 p.Pro289=
c.867C>T · rs61755279 · VCV2640855
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.924%, 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 -20 | GERP -4.9 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.924%
Middle Eastern · 56/6,062 alleles
Filtering AF
0.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.661%
Overall
0.162%
2,615/1,614,182 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.924% | 108 |
| South Asian | 0.648% | 154 |
| Admixed American | 0.26% | 385 |
| Remaining individualsnot grpmax-eligible | 0.208% | 481 |
| European (non-Finnish) | 0.139% | 721 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0439% | 2,277 |
| African / African-American | 0.0293% | 3,411 |
| Finnishnot grpmax-eligible | 0.0156% | 6,404 |
| East Asian | 0.00223% | 44,886 |
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
- CASP7
- Protein
- p.Pro289=
- Coding
- c.867C>T
- MANE Select
- NM_001227
- dbSNP
- rs61755279
- Type
- single nucleotide variant
- Location
- chr10:113729495 (GRCh38)
- Gene constraint
- LOEUF 0.993 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.05 · 47 PDB
Similar variants
- CASP7 p.Pro289Ser Uncertain significance ★ ⚠ same residue
- CASP7 p.Pro289Thr Uncertain significance ★ ⚠ same residue
- CASP7 p.Asp255Glu Benign ★★ same type
- CASP7 p.Ala164Val Uncertain significance ★ ⚠ same type
- CASP7 p.Ala270Ser Uncertain significance ★ ⚠ same type
- CASP7 p.Ala270Val Uncertain significance ★ ⚠ same type
- CASP7 p.Arg210Gln Uncertain significance ★ ⚠ same type
- CASP7 p.Arg28Gln 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/casp7-p-pro289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown