ARHGAP4 p.Pro627=
c.1881G>A · rs200936669 · VCV711791
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.39%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.39%
African / African-American · 2,500/56,929 alleles
Filtering AF
4.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.19%
Overall
0.245%
2,947/1,203,617 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.39% | 23 |
| Admixed American | 0.423% | 237 |
| Remaining individualsnot grpmax-eligible | 0.363% | 275 |
| Middle Eastern | 0.192% | 520 |
| European (non-Finnish) | 0.00794% | 12,590 |
| South Asian | 0.00532% | 18,810 |
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
- ARHGAP4
- Protein
- p.Pro627=
- Coding
- c.1881G>A
- MANE Select
- NM_001666
- dbSNP
- rs200936669
- Type
- single nucleotide variant
- Location
- chrX:153910547 (GRCh38)
- Structure
- AlphaFold pLDDT 76.48 · 1 PDB
- Residue 627
- the rho-gap domain
Similar variants
- ARHGAP4 p.Val705Ile Uncertain significance ★★ ⚠ same type
- ARHGAP4 c.2415-4G>A Benign ★★ same type
- ARHGAP4 c.2608-6C>T Benign ★★ same type
- ARHGAP4 p.Asp420= Benign ★★ same type
- ARHGAP4 p.His572= Benign ★★ same type
- ARHGAP4 c.682-292A>C Uncertain significance ★ same type
- ARHGAP4 c.682-302C>G Uncertain significance ★ same type
- ARHGAP4 c.682-331G>A 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/arhgap4-p-pro627 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown