PAK3 p.Arg239=
c.717G>A · rs1420523796 · VCV588634
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0153%, amr)
Conditions
1
Inborn genetic diseases
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 1.2 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 5.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0153%
Admixed American · 7/45,625 alleles
Filtering AF
0.00715%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00508%
Overall
0.000914%
11/1,202,944 alleles · ultra-rare
exomes 7/1,091,766 · genomes 4/111,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0153% | 6,518 |
| Remaining individualsnot grpmax-eligible | 0.00633% | 15,792 |
| African / African-American | 0.00176% | 56,879 |
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
- PAK3
- Protein
- p.Arg239=
- Coding
- c.717G>A
- MANE Select
- NM_002578
- dbSNP
- rs1420523796
- Type
- single nucleotide variant
- Location
- chrX:111163678 (GRCh38)
- Structure
- AlphaFold pLDDT 66.31 · 4 PDB
- Residue 239
- the sh3 domain; a β-strand
Similar variants
- PAK3 p.Arg436Ter Pathogenic/Likely pathogenic ★★ same condition
- PAK3 c.830+6T>A Uncertain significance ★★ same condition
- PAK3 c.276+2659T>C Benign/Likely benign ★★ same condition
- PAK3 p.Ala161= Benign/Likely benign ★★ same condition
- PAK3 p.Asn236Ser Likely benign ★★ same condition
- PAK3 p.Gly4Ser Benign/Likely benign ★★ same condition
- PAK3 p.Leu395= Benign ★★ same condition
- PAK3 p.Ser224Tyr Benign/Likely benign ★★ same condition
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/pak3-p-arg239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown