ARHGAP1 p.Pro52=
c.156G>A · rs554016754 · VCV726522
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.601%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.106 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -2.5 |
| Overall | ||
| CADD | 2.588 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.601%
South Asian · 506/84,162 alleles
Filtering AF
0.558%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.541%
Overall
0.0365%
567/1,552,216 alleles · rare
exomes 519/1,399,898 · genomes 48/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.601% | 166 |
| Remaining individualsnot grpmax-eligible | 0.0366% | 2,735 |
| Middle Eastern | 0.0167% | 5,986 |
| European (non-Finnish) | 0.00314% | 31,866 |
| African / African-American | 0.00273% | 36,587 |
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
- ARHGAP1
- Protein
- p.Pro52=
- Coding
- c.156G>A
- MANE Select
- NM_004308
- dbSNP
- rs554016754
- Type
- single nucleotide variant
- Location
- chr11:46695733 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 82.64 · 11 PDB
- Residue 52
- the 'disordered' region
Similar variants
- ARHGAP1 p.Leu263Phe Benign ★★ same type
- ARHGAP1 p.Ala225Ser Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Ala26Val Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Ala373Thr Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Ala68Pro Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Arg234Gln Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Arg234Trp Uncertain significance ★ ⚠ same type
- ARHGAP1 p.Arg349Trp 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/arhgap1-p-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown