Is TYK2 p.Gln509Arg (c.1526A>G) pathogenic?

TYK2 p.Gln509Arg (c.1526A>G) is classified Uncertain significance in TYK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). AlphaMissense: likely benign (0.0783); Very rare (popmax 0.00167%, amr); Associated with Inborn genetic diseases.

What condition is associated with TYK2 p.Gln509Arg (c.1526A>G)?

TYK2 p.Gln509Arg (c.1526A>G) is associated with Inborn genetic diseases (ClinVar).

How common is TYK2 p.Gln509Arg (c.1526A>G) in the general population?

TYK2 p.Gln509Arg (c.1526A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about TYK2 p.Gln509Arg (c.1526A>G)?

AlphaMissense predicts likely benign (score 0.0783) — an in-silico prediction, not a clinical call.

TYK2 p.Gln509Arg

c.1526A>G · VCV4194461

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0783 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0783	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -6.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP -1.6, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 28 kb · p 6.7e-09 · regional, not allelic
Overall
CADD	13.61	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

Grpmax group 0.00167% Admixed American · 1/59,890 alleles

Overall 6.85e-05% 1/1,460,114 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: TYK2
Protein: p.Gln509Arg
Coding: c.1526A>G
MANE Select: NM_003331
Type: single nucleotide variant
Location: chr19:10362407 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.69 · 52 PDB
Residue 509: the sh2; atypical domain

Full TYK2 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

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TYK2 p.Ala671Thr Uncertain significance ★★ ⚠ same condition
TYK2 p.Arg269His Uncertain significance ★★ ⚠ same condition
TYK2 p.Arg274Cys Uncertain significance ★★ ⚠ same condition
TYK2 p.Arg294Trp Uncertain significance ★★ ⚠ same condition
TYK2 p.Arg410Trp 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/tyk2-p-gln509arg (accessed [today's date]).

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