PAK5 p.Val172=
c.516A>G · rs115731613 · VCV790215
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.7%, 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 -9.6 | GERP -5.2 |
| Overall | ||
| CADD | 0.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.7%
African / African-American · 2,028/75,006 alleles
Filtering AF
2.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.57%
Overall
0.142%
2,287/1,614,076 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.7% | 37 |
| Remaining individualsnot grpmax-eligible | 0.189% | 530 |
| Admixed American | 0.17% | 588 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.011% | 9,108 |
| European (non-Finnish) | 0.00178% | 56,190 |
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
- PAK5
- Protein
- p.Val172=
- Coding
- c.516A>G
- MANE Select
- NM_177990
- dbSNP
- rs115731613
- Type
- single nucleotide variant
- Location
- chr20:9580619 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.09 · 2 PDB
- Residue 172
- the 'linker' region
Similar variants
- PAK5 p.Leu490= Benign ★★ same type
- PAK5 p.Leu603= Benign ★★ same type
- PAK5 p.Lys216= Benign ★★ same type
- PAK5 p.Tyr333= Benign ★★ same type
- PAK5 p.Ala120Gly Uncertain significance ★ ⚠ same type
- PAK5 p.Ala120Val Uncertain significance ★ ⚠ same type
- PAK5 p.Ala251Val Uncertain significance ★ ⚠ same type
- PAK5 p.Ala303Thr 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/pak5-p-val172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown