ARHGAP4 p.Asp420=
c.1260C>T · rs149100821 · VCV774976
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, nfe)
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 1.3 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 8.279 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
European (non-Finnish) · 10,335/895,290 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.924%
11,185/1,210,639 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.15% | 87 |
| Remaining individualsnot grpmax-eligible | 0.815% | 123 |
| Finnishnot grpmax-eligible | 0.363% | 276 |
| Admixed American | 0.322% | 310 |
| Middle Eastern | 0.184% | 544 |
| Amishnot grpmax-eligible | 0.146% | 684 |
| African / African-American | 0.127% | 788 |
| South Asian | 0.107% | 932 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00908% | 11,017 |
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
- ARHGAP4
- Protein
- p.Asp420=
- Coding
- c.1260C>T
- MANE Select
- NM_001666
- dbSNP
- rs149100821
- Type
- single nucleotide variant
- Location
- chrX:153913475 (GRCh38)
- Structure
- AlphaFold pLDDT 76.48 · 1 PDB
- Residue 420
- the 'disordered' region
Similar variants
- ARHGAP4 p.Val705Ile Uncertain significance ★★ ⚠ same type
- ARHGAP4 c.2415-4G>A Benign ★★ same type
- ARHGAP4 c.2608-6C>T Benign ★★ same type
- ARHGAP4 p.His572= Benign ★★ same type
- ARHGAP4 p.Pro627= Benign ★★ same type
- ARHGAP4 c.682-292A>C Uncertain significance ★ same type
- ARHGAP4 c.682-302C>G Uncertain significance ★ same type
- ARHGAP4 c.682-331G>A 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/arhgap4-p-asp420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown