PAK1 p.Ser115=
c.345G>A · rs367836292 · VCV712103
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.01%, sas)
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 -4.9 | GERP -3.8 |
| Overall | ||
| CADD | 11.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.01%
South Asian · 1,828/91,030 alleles
Filtering AF
1.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9%
Overall
0.122%
1,966/1,613,852 alleles · low-frequency
exomes 1,850/1,461,612 · genomes 116/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.01% | 50 |
| Remaining individualsnot grpmax-eligible | 0.168% | 595 |
| Middle Eastern | 0.0838% | 1,193 |
| Admixed American | 0.0117% | 8,571 |
| African / African-American | 0.008% | 12,504 |
| East Asian | 0.00446% | 22,435 |
| European (non-Finnish) | 0.0011% | 90,766 |
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
- PAK1
- Protein
- p.Ser115=
- Coding
- c.345G>A
- MANE Select
- NM_002576
- dbSNP
- rs367836292
- Type
- single nucleotide variant
- Location
- chr11:77379335 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 73.90 · 41 PDB
- Residue 115
- a modified residue (phosphoserine); the 'autoregulatory region' region; an α-helix
Similar variants
- PAK1 p.Ser115Leu Uncertain significance ★ ⚠ same residue
- PAK1 p.Ile476Thr Pathogenic/Likely pathogenic ★★ same type
- PAK1 p.Leu470Arg Likely pathogenic ★★ same type
- PAK1 p.Met143Thr Likely pathogenic ★★ same type
- PAK1 p.Pro121Leu Pathogenic ★★ same type
- PAK1 p.Pro121Ser Pathogenic/Likely pathogenic ★★ same type
- PAK1 p.Ala524Pro Uncertain significance ★★ ⚠ same type
- PAK1 p.Arg215Trp 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/pak1-p-ser115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown