ARHGAP21 p.Thr770=
c.2310C>T · rs367801923 · VCV2640355
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 3 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 5.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/60,010 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.00136%
22/1,614,072 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 6,001 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,811 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000254% | 393,348 |
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
- ARHGAP21
- Protein
- p.Thr770=
- Coding
- c.2310C>T
- MANE Select
- NM_020824
- dbSNP
- rs367801923
- Type
- single nucleotide variant
- Location
- chr10:24619585 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 45.03 · 3 PDB
Similar variants
- ARHGAP21 p.Thr770Ile Uncertain significance ★ ⚠ same residue
- ARHGAP10 p.Asn222Ser Uncertain significance ★★ ⚠ same type
- ARHGAP10 p.Ala405= Benign ★★ same type
- ARHGAP10 p.Arg243= Benign ★★ same type
- ARHGAP10 p.Ile676Val Likely benign ★★ same type
- ARHGAP10 p.Ser487= Benign ★★ same type
- ARHGAP10 p.Tyr614= Benign ★★ same type
- ARHGAP21 p.Cys1016Ser Likely benign ★★ 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/arhgap21-p-thr770 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown