PAK3 p.Ser260=
c.780T>C · rs1569440808 · VCV588162
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.82e-05%)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.30 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 13.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.82e-05%
Overall
8.82e-05%
1/1,133,754 alleles · very rare
exomes 1/1,020,934 · genomes 0/112,820 · joint denominator
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.Ser260=
- Coding
- c.780T>C
- MANE Select
- NM_002578
- dbSNP
- rs1569440808
- Type
- single nucleotide variant
- Location
- chrX:111173031 (GRCh38)
- Structure
- AlphaFold pLDDT 66.31 · 4 PDB
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-ser260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown