ARHGAP31 p.Ala852=
c.2556T>C · rs2472876155 · VCV2102696
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 0.13 | GERP -2.3, phastCons 0.13 |
| Overall | ||
| CADD | 6.015 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,886 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000205%
3/1,461,892 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,886 |
| European (non-Finnish) | 0.000169% | 590,019 |
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.Ala852=
- Coding
- c.2556T>C
- MANE Select
- NM_020754
- dbSNP
- rs2472876155
- Type
- single nucleotide variant
- Location
- chr3:119414485 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
- Residue 852
- 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-ala852 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown