PAK3 p.Arg436Ter
c.1306C>T · VCV3376283
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 0.27, phastCons 1 |
| Overall | ||
| CADD | 36.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PAK3
- Protein
- p.Arg436Ter
- Coding
- c.1306C>T
- MANE Select
- NM_001354046 · reported on NM_002578
- Type
- single nucleotide variant
- Location
- chrX:111196539 (GRCh38)
- Structure
- AlphaFold pLDDT 66.31 · 4 PDB
- Residue 436
- the dh domain; an α-helix
Similar variants
- PAK3 p.Arg100Ter Pathogenic/Likely pathogenic ★★ same condition
- PAK3 p.Glu356Ter Pathogenic/Likely pathogenic ★★ same condition
- PAK3 c.830+6T>A Uncertain significance ★★ same condition
- PAK3 p.Arg493Cys Uncertain significance ★★ ⚠ same condition
- PAK3 p.Gly262= Uncertain significance ★★ same condition
- PAK3 p.Gly335Asp Uncertain significance ★★ ⚠ same condition
- PAK3 c.276+2659T>C Benign/Likely benign ★★ same condition
- PAK3 c.431-26A>G 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-arg436ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown