ARHGAP31 p.Leu602del
c.1804_1806del · VCV4963712
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP -0.53, phastCons 1 |
| Overall | ||
| CADD | 5.498 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,874 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.00031%
5/1,612,856 alleles · very rare
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.Leu602del
- Coding
- c.1804_1806del
- MANE Select
- NM_020754
- Type
- Deletion
- Location
- chr3:119409653 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
- Residue 602
- the 'disordered' region
Similar variants
- ARHGAP31 c.100+19del Benign/Likely benign ★★ same type
- ARHGAP31 p.Pro567fs Likely pathogenic ★ same type
- ARHGAP31 c.882-11_882-5del Uncertain significance ★ same type
- ARHGAP31 p.Cys1424fs Uncertain significance ★ same type
- ARHGAP31 p.Gly49fs Uncertain significance ★ same type
- ARHGAP31 p.Leu1050_His1052del Conflicting classifications of pathogenicity ★ same type
- ARHGAP31 p.Pro739fs Uncertain significance ★ same type
- ARHGAP31 p.Ser1432_Val1433insTer 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-leu602del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown