Is ITK p.Ala281Ser (c.841G>T) pathogenic?

ITK p.Ala281Ser (c.841G>T) is classified Uncertain significance in ITK (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-11). AlphaMissense: likely benign (0.1408); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ITK p.Ala281Ser (c.841G>T)?

ITK p.Ala281Ser (c.841G>T) is associated with Inborn genetic diseases (ClinVar).

How common is ITK p.Ala281Ser (c.841G>T) in the general population?

ITK p.Ala281Ser (c.841G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ITK p.Ala281Ser (c.841G>T)?

AlphaMissense predicts likely benign (score 0.1408) — an in-silico prediction, not a clinical call.

ITK p.Ala281Ser

c.841G>T · VCV3530784

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1408 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1408	likely benign
REVEL	0.478	indeterminate
SaProt	LLR -5.66	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 0.98, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 63 kb · p 2.1e-06 · regional, not allelic
Overall
CADD	21.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: ITK
Protein: p.Ala281Ser
Coding: c.841G>T
MANE Select: NM_005546
Type: single nucleotide variant
Location: chr5:157238181 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.82 · 37 PDB
Residue 281: 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.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
ITK p.Leu612Met 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-ala281ser (accessed [today's date]).

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