ARHGAP21 p.Val1165=
c.3495T>A · rs144834281 · VCV725284
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.265%, afr)
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 4.5 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 10.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.265%
African / African-American · 198/74,676 alleles
Filtering AF
0.235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.223%
Overall
0.0188%
301/1,603,840 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.265% | 377 |
| Middle Eastern | 0.0332% | 3,010 |
| Remaining individualsnot grpmax-eligible | 0.0274% | 3,654 |
| Admixed American | 0.0119% | 8,425 |
| European (non-Finnish) | 0.0063% | 15,866 |
| South Asian | 0.00336% | 29,739 |
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
- ARHGAP21
- Protein
- p.Val1165=
- Coding
- c.3495T>A
- MANE Select
- NM_020824
- dbSNP
- rs144834281
- Type
- single nucleotide variant
- Location
- chr10:24596026 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 45.03 · 3 PDB
- Residue 1165
- the rho-gap domain
Similar variants
- ARHGAP10 p.Asn222Ser Uncertain significance ★★ ⚠ same type
- ARHGAP10 p.Ala405= Benign ★★ same type
- ARHGAP10 p.Arg243= Benign ★★ same type
- ARHGAP10 p.Ile676Val Likely benign ★★ same type
- ARHGAP10 p.Ser487= Benign ★★ same type
- ARHGAP10 p.Tyr614= Benign ★★ same type
- ARHGAP21 p.Cys1016Ser Likely benign ★★ same type
- ARHGAP21 p.Gly1121Ser 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/arhgap21-p-val1165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown