ARHGAP4 p.Arg430=
c.1290C>T · rs145134760 · VCV714975
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.347%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.89 | GERP -3.7, phastCons 0.002 |
| Overall | ||
| CADD | 3.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.347%
African / African-American · 199/57,424 alleles
Filtering AF
0.307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.292%
Overall
0.0197%
238/1,209,943 alleles · rare
exomes 117/1,097,474 · genomes 121/112,469 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.347% | 289 |
| East Asian | 0.0267% | 3,751 |
| Middle Eastern | 0.023% | 4,341 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,802 |
| Admixed American | 0.00872% | 11,470 |
| European (non-Finnish) | 0.0019% | 52,647 |
| South Asian | 0.00176% | 56,794 |
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.Arg430=
- Coding
- c.1290C>T
- MANE Select
- NM_001666
- dbSNP
- rs145134760
- Type
- single nucleotide variant
- Location
- chrX:153913445 (GRCh38)
- Structure
- AlphaFold pLDDT 76.48 · 1 PDB
- Residue 430
- the 'disordered' region
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-arg430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown