ARHGAP32 p.Pro248=
c.744C>T · rs899696871 · VCV2642542
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00179%, 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 1.9 | GERP -0.98, phastCons 1 |
| Overall | ||
| CADD | 12.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00179%
European (non-Finnish) · 21/1,171,018 alleles
Filtering AF
0.00115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000978%
Overall
0.0015%
24/1,595,926 alleles · very rare
exomes 24/1,443,790 · genomes 0/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00179% | 55,763 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,850 |
| African / African-American | 0.00134% | 74,554 |
| South Asian | 0.00114% | 87,536 |
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
- ARHGAP32
- Protein
- p.Pro248=
- Coding
- c.744C>T
- MANE Select
- NM_001378024
- dbSNP
- rs899696871
- Type
- single nucleotide variant
- Location
- chr11:129064859 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 43.67 · 2 PDB
Similar variants
- ARHGAP32 c.360-10T>C Benign/Likely benign ★★ same type
- ARHGAP32 p.Ala1413= Benign ★★ same type
- ARHGAP32 p.Ala2078= Likely benign ★★ same type
- ARHGAP32 p.Arg1412= Benign ★★ same type
- ARHGAP32 p.Arg1629= Likely benign ★★ same type
- ARHGAP32 p.Arg1726Trp Benign ★★ same type
- ARHGAP32 p.Glu1154Gly Benign ★★ same type
- ARHGAP32 p.Glu390= Benign ★★ 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/arhgap32-p-pro248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown