Is ITK p.Tyr305fs (c.913del) pathogenic?

ITK p.Tyr305fs (c.913del) is classified Pathogenic in ITK (ClinVar, Single submitter, 1 submitter; last evaluated 2016-07-28). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with ITK p.Tyr305fs (c.913del)?

ITK p.Tyr305fs (c.913del) is associated with Inborn genetic diseases (ClinVar).

How common is ITK p.Tyr305fs (c.913del) in the general population?

ITK p.Tyr305fs (c.913del) is absent from gnomAD (gnomAD).

ITK p.Tyr305fs

c.913del · rs1554102738 · VCV521210

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 10 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.6	GERP -3.7

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ITK
Protein: p.Tyr305fs
Coding: c.913del
MANE Select: NM_005546
dbSNP: rs1554102738
Type: Deletion
Location: chr5:157240123 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.82 · 37 PDB
Residue 305: the sh2 domain

Full ITK gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITK p.Tyr305= Likely benign ★★ same residue
ITK p.Ala308Ser Uncertain significance ★★ ⚠ same condition
ITK p.Arg451Trp Uncertain significance ★★ ⚠ same condition
ITK p.Arg602Trp Uncertain significance ★★ ⚠ same condition
ITK p.Glu196Gln Uncertain significance ★★ ⚠ same condition
ITK p.His378Arg Uncertain significance ★★ ⚠ same condition
ITK p.His586Asp Uncertain significance ★★ ⚠ same condition
ITK p.Ile590Met Uncertain significance ★★ ⚠ 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/itk-p-tyr305fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown