ITK p.Arg342=
c.1026G>A · VCV3388877
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 · G>C here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.087 | GERP -2.4, phastCons 0.076 |
| Overall | ||
| CADD | 8.821 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,864 alleles
Overall
6.84e-05%
1/1,461,642 alleles · very rare
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
- ITK
- Protein
- p.Arg342=
- Coding
- c.1026G>A
- MANE Select
- NM_005546
- Type
- single nucleotide variant
- Location
- chr5:157241686 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.82 · 37 PDB
Similar variants
- ITK p.Arg562Ter Pathogenic/Likely pathogenic ★★ same type
- ITK c.851+5G>A Uncertain significance ★★ same type
- ITK p.Ala191Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala261Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala308Ser Uncertain significance ★★ ⚠ same type
- ITK p.Ala345Val Uncertain significance ★★ ⚠ same type
- ITK p.Ala471Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala525Thr 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/itk-p-arg342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown