ARHGAP4 p.Pro739=
c.2217C>A · rs549301187 · VCV2661753
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00527%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.023 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.8 | GERP -2.1 |
| Overall | ||
| CADD | 0.114 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00527%
South Asian · 3/56,976 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000687%
Overall
0.0014%
17/1,211,285 alleles · very rare
exomes 17/1,097,472 · genomes 0/113,813 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00527% | 18,992 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,629 |
| European (non-Finnish) | 0.00145% | 68,880 |
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.Pro739=
- Coding
- c.2217C>A
- MANE Select
- NM_001666
- dbSNP
- rs549301187
- Type
- single nucleotide variant
- Location
- chrX:153910025 (GRCh38)
- Structure
- AlphaFold pLDDT 76.48 · 1 PDB
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-pro739 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown