PAK3 p.Thr79=
c.237G>A · rs768688720 · VCV1663674
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00217%, 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 0.046 | GERP 0.26, phastCons 0.58 |
| Overall | ||
| CADD | 9.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/46,001 alleles
Filtering AF
9.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5e-05%
Overall
0.000422%
5/1,185,836 alleles · very rare
exomes 5/1,072,066 · genomes 0/113,770 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00217% | 46,001 |
| Remaining individualsnot grpmax-eligible | 0.00214% | 46,785 |
| European (non-Finnish) | 0.000344% | 290,581 |
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.Thr79=
- Coding
- c.237G>A
- MANE Select
- NM_002578
- dbSNP
- rs768688720
- Type
- single nucleotide variant
- Location
- chrX:111142157 (GRCh38)
- Structure
- AlphaFold pLDDT 66.31 · 4 PDB
- Residue 79
- the calponin-homology (ch) domain; an α-helix
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-thr79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown