ARHGAP31 p.Pro513=
c.1539G>A · rs753289468 · VCV1915735
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -5.2 |
| Overall | ||
| CADD | 0.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00149%
24/1,614,116 alleles · ultra-rare
exomes 18/1,461,864 · genomes 6/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| African / African-American | 0.00267% | 37,471 |
| Admixed American | 0.00167% | 60,014 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
| European (non-Finnish) | 0.00119% | 84,290 |
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
- ARHGAP31
- Protein
- p.Pro513=
- Coding
- c.1539G>A
- MANE Select
- NM_020754
- dbSNP
- rs753289468
- Type
- single nucleotide variant
- Location
- chr3:119402291 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
- Residue 513
- the 'disordered' region
Similar variants
- ARHGAP31 p.Pro513Ala Uncertain significance ★★ ⚠ same residue
- ARHGAP31 p.Pro513Leu Uncertain significance ★ ⚠ same residue
- ARHGAP31 p.Ala18Val Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Ala634Asp Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg1377Ser Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg199Gln Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg256Cys Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg426Gly 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/arhgap31-p-pro513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown