ARHGAP31 p.Pro1085=
c.3255C>T · rs372301689 · VCV282082
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.118%, eas)
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 0.23 | GERP -1.1 |
| Overall | ||
| CADD | 7.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.118%
East Asian · 53/44,886 alleles
Filtering AF
0.0927%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0836%
Overall
0.00589%
95/1,614,158 alleles · rare
exomes 80/1,461,892 · genomes 15/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.118% | 847 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| Finnishnot grpmax-eligible | 0.00781% | 12,803 |
| South Asian | 0.00659% | 15,179 |
| African / African-American | 0.00267% | 37,513 |
| European (non-Finnish) | 0.00161% | 62,107 |
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.Pro1085=
- Coding
- c.3255C>T
- MANE Select
- NM_020754
- dbSNP
- rs372301689
- Type
- single nucleotide variant
- Location
- chr3:119415184 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
- Residue 1085
- the 'disordered' region
Similar variants
- 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
- ARHGAP31 p.Arg478His Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg510Ser 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-pro1085 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown