Is TYK2 p.Phe1003= (c.3009C>T) pathogenic?

TYK2 p.Phe1003= (c.3009C>T) is classified Likely benign in TYK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-24). Very rare (popmax 0.00876%, amr); Associated with immunodeficiency 35.

What condition is associated with TYK2 p.Phe1003= (c.3009C>T)?

TYK2 p.Phe1003= (c.3009C>T) is associated with immunodeficiency 35 (ClinVar).

How common is TYK2 p.Phe1003= (c.3009C>T) in the general population?

TYK2 p.Phe1003= (c.3009C>T) is very rare (popmax 0.00876%, amr) (gnomAD).

TYK2 p.Phe1003=

Q: How is Susceptibility to infection due to TYK2 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.3009C>T · rs760083588 · VCV1124740

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00876%, amr)

Conditions

immunodeficiency 35

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.36	GERP -1.5, phastCons 0.004
Overall
CADD	10.36	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00876% Admixed American · 4/45,650 alleles

Filtering AF 0.00294% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00178%

Overall 0.000534% 8/1,499,286 alleles · very rare exomes 8/1,347,002 · genomes 0/152,284 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00876%	11,413
Remaining individualsnot grpmax-eligible	0.00174%	57,594
European (non-Finnish)	0.000268%	373,452

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.Phe1003=
Coding: c.3009C>T
MANE Select: NM_003331
dbSNP: rs760083588
Type: single nucleotide variant
Location: chr19:10353546 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.69 · 52 PDB
Residue 1003: an α-helix; the protein kinase 2 domain

Full TYK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 35 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Susceptibility to infection due to TYK2 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

TYK2 p.Arg609Ter Pathogenic/Likely pathogenic ★★ same condition
TYK2 p.Trp798Ter Pathogenic ★★ same condition
TYK2 p.Ala1004Gly Uncertain significance ★★ ⚠ same condition
TYK2 p.Ala1026Thr Uncertain significance ★★ ⚠ same condition
TYK2 p.Ala165Thr Uncertain significance ★★ ⚠ same condition
TYK2 p.Ala195Ser Uncertain significance ★★ ⚠ same condition
TYK2 p.Ala195Thr Uncertain significance ★★ same condition
TYK2 p.Ala413Val 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-phe1003 (accessed [today's date]).

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