CRIP2 p.Asp169=
c.507C>T · rs112961323 · VCV729187
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.576%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.092 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.9 | GERP -3.7 |
| Overall | ||
| CADD | 1.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.576%
African / African-American · 432/75,040 alleles
Filtering AF
0.531%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.513%
Overall
0.0301%
485/1,612,802 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.576% | 174 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| Admixed American | 0.0317% | 3,159 |
| South Asian | 0.00549% | 18,215 |
| East Asian | 0.00223% | 44,882 |
| European (non-Finnish) | 0.000254% | 393,320 |
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
- CRIP2
- Protein
- p.Asp169=
- Coding
- c.507C>T
- MANE Select
- NM_001312
- dbSNP
- rs112961323
- Type
- single nucleotide variant
- Location
- chr14:105479441 (GRCh38)
- Gene constraint
- LOEUF 1.553 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.78 · 1 PDB
- Residue 169
- the lim zinc-binding 2 domain
Similar variants
- CRIP2 p.Ala113Val Uncertain significance ★ ⚠ same type
- CRIP2 p.Ala166Thr Uncertain significance ★ ⚠ same type
- CRIP2 p.Ala82Thr Uncertain significance ★ ⚠ same type
- CRIP2 p.Ala96Gly Uncertain significance ★ ⚠ same type
- CRIP2 p.Ala98Thr Uncertain significance ★ ⚠ same type
- CRIP2 p.Arg128His Uncertain significance ★ ⚠ same type
- CRIP2 p.Arg148Gly Uncertain significance ★ ⚠ same type
- CRIP2 p.Arg148Trp 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/crip2-p-asp169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown