ARHGAP4 p.Pro803=
c.2409C>T · rs374821227 · VCV2661751
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0206%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0206%
European (non-Finnish) · 182/884,620 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0172%
Overall
0.0168%
200/1,187,801 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0206% | 4,861 |
| East Asian | 0.018% | 5,563 |
| Remaining individualsnot grpmax-eligible | 0.0107% | 9,328 |
| South Asian | 0.00751% | 13,308 |
| Admixed American | 0.00459% | 21,784 |
| African / African-American | 0.00175% | 57,088 |
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.Pro803=
- Coding
- c.2409C>T
- MANE Select
- NM_001666
- dbSNP
- rs374821227
- Type
- single nucleotide variant
- Location
- chrX:153909746 (GRCh38)
- Structure
- AlphaFold pLDDT 76.48 · 1 PDB
- Residue 803
- the sh3 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 p.Pro627= Benign ★★ same type
- ARHGAP4 c.682-292A>C Uncertain significance ★ same type
- ARHGAP4 c.682-302C>G 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-pro803 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown