ARHGAP36 p.Arg439=
c.1317C>T · VCV4642423
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.035%, afr)
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 0.029 | GERP -3, phastCons 0.97 |
| Overall | ||
| CADD | 1.169 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.035%
African / African-American · 20/57,146 alleles
Filtering AF
0.0232%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0194%
Overall
0.00347%
42/1,210,171 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.035% | 2,857 |
| Remaining individualsnot grpmax-eligible | 0.0105% | 9,525 |
| South Asian | 0.00528% | 18,936 |
| Admixed American | 0.00436% | 22,924 |
| Finnishnot grpmax-eligible | 0.00215% | 46,569 |
| European (non-Finnish) | 0.00123% | 81,393 |
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
- ARHGAP36
- Protein
- p.Arg439=
- Coding
- c.1317C>T
- MANE Select
- NM_144967
- Type
- single nucleotide variant
- Location
- chrX:131086364 (GRCh38)
- Structure
- AlphaFold pLDDT 68.40
Similar variants
- ARHGAP36 p.Lys295Arg Uncertain significance ★★ ⚠ same type
- ARHGAP36 c.-200A>G Uncertain significance ★ same type
- ARHGAP36 p.Ala11Glu Uncertain significance ★ ⚠ same type
- ARHGAP36 p.Ala13Val Uncertain significance ★ ⚠ same type
- ARHGAP36 p.Ala200Asp Uncertain significance ★ ⚠ same type
- ARHGAP36 p.Ala200Val Uncertain significance ★ ⚠ same type
- ARHGAP36 p.Ala38Pro Uncertain significance ★ ⚠ same type
- ARHGAP36 p.Ala417Val 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/arhgap36-p-arg439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown