CIMIP2A p.Arg75=
c.225G>A · rs61729153 · VCV3067274
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.347%, nfe)
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 -2.7 | GERP -1.2 |
| Overall | ||
| CADD | 0.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.347%
European (non-Finnish) · 4,071/1,174,470 alleles
Filtering AF
0.338%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.334%
Overall
0.276%
4,436/1,605,368 alleles · rare
exomes 4,164/1,453,100 · genomes 272/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.347% | 288 |
| Remaining individualsnot grpmax-eligible | 0.272% | 367 |
| Admixed American | 0.181% | 552 |
| African / African-American | 0.0521% | 1,920 |
| Finnishnot grpmax-eligible | 0.0458% | 2,181 |
| Middle Eastern | 0.0332% | 3,016 |
| South Asian | 0.0188% | 5,312 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00344% | 29,092 |
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
- CIMIP2A
- Protein
- p.Arg75=
- Coding
- c.225G>A
- MANE Select
- NM_001001710
- dbSNP
- rs61729153
- Type
- single nucleotide variant
- Location
- chr9:137245685 (GRCh38)
- Structure
- AlphaFold pLDDT 61.88
Similar variants
- STPG3 p.Ser126Gly Benign ★★ same type
- CIMIP2A p.Ala187Pro Uncertain significance ★ ⚠ same type
- CIMIP2A p.Ala215Val Uncertain significance ★ ⚠ same type
- CIMIP2A p.Ala241Val Uncertain significance ★ ⚠ same type
- CIMIP2A p.Ala311Thr Uncertain significance ★ ⚠ same type
- CIMIP2A p.Arg188Cys Uncertain significance ★ ⚠ same type
- CIMIP2A p.Arg189Cys Uncertain significance ★ ⚠ same type
- CIMIP2A p.Arg189His 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/cimip2a-p-arg75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown