PAK3 p.Ser156=
c.468G>A · rs143591118 · VCV732543
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0941%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.40 | donor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -0.2, phastCons 1 |
| Overall | ||
| CADD | 19.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0941%
Middle Eastern · 4/4,252 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0194%
Overall
0.017%
196/1,156,194 alleles · ultra-rare
exomes 184/1,044,775 · genomes 12/111,419 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0941% | 1,063 |
| European (non-Finnish) | 0.022% | 4,553 |
| Remaining individualsnot grpmax-eligible | 0.00655% | 15,264 |
| African / African-American | 0.00357% | 27,998 |
| Admixed American | 0.00219% | 45,594 |
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.Ser156=
- Coding
- c.468G>A
- MANE Select
- NM_002578
- dbSNP
- rs143591118
- Type
- single nucleotide variant
- Location
- chrX:111152447 (GRCh38)
- Structure
- AlphaFold pLDDT 66.31 · 4 PDB
Similar variants
- PAK3 p.Ser156Leu Likely benign ★ same residue
- PAK3 p.Arg100Ter Pathogenic/Likely pathogenic ★★ same type
- PAK3 p.Arg436Ter Pathogenic/Likely pathogenic ★★ same type
- PAK3 p.Glu356Ter Pathogenic/Likely pathogenic ★★ same type
- PAK3 c.830+6T>A Uncertain significance ★★ same type
- PAK3 p.Ala490Thr Uncertain significance ★★ ⚠ same type
- PAK3 p.Arg493Cys Uncertain significance ★★ ⚠ same type
- PAK3 p.Arg498Cys 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/pak3-p-ser156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown