ARHGAP31 p.Gln75=
c.225A>G · rs142578368 · VCV727075
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, 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 1.9 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 9.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,062 alleles
Filtering AF
0.0333%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0291%
Overall
0.00446%
72/1,614,200 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,021 |
| African / African-American | 0.0453% | 2,208 |
| Admixed American | 0.0183% | 5,458 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| European (non-Finnish) | 0.00153% | 65,556 |
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.Gln75=
- Coding
- c.225A>G
- MANE Select
- NM_020754
- dbSNP
- rs142578368
- Type
- single nucleotide variant
- Location
- chr3:119368393 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
- Residue 75
- the rho-gap domain
Similar variants
- ARHGAP31 p.Gln75Lys 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
- ARHGAP31 p.Arg478His 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-gln75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown