Is TYK2 p.Pro834= (c.2502C>T) pathogenic?

TYK2 p.Pro834= (c.2502C>T) is classified Likely benign in TYK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-06). Ultra-rare (popmax 0.0169%, mid); Associated with immunodeficiency 35.

What condition is associated with TYK2 p.Pro834= (c.2502C>T)?

TYK2 p.Pro834= (c.2502C>T) is associated with immunodeficiency 35 (ClinVar).

How common is TYK2 p.Pro834= (c.2502C>T) in the general population?

TYK2 p.Pro834= (c.2502C>T) is ultra-rare (popmax 0.0169%, mid) (gnomAD).

TYK2 p.Pro834=

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.2502C>T · rs376003056 · VCV1582840

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0169%, mid)

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 -14	GERP -3.7
Overall
CADD	0.192	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0169% Middle Eastern · 1/5,934 alleles

Filtering AF 0.0052% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00474%

Overall 0.00534% 86/1,611,166 alleles · ultra-rare exomes 80/1,459,056 · genomes 6/152,110 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0169%	5,934
Remaining individualsnot grpmax-eligible	0.00643%	15,554
European (non-Finnish)	0.00636%	15,721
East Asian	0.00446%	22,398
African / African-American	0.00401%	24,948
South Asian	0.0011%	90,704

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.Pro834=
Coding: c.2502C>T
MANE Select: NM_003331
dbSNP: rs376003056
Type: single nucleotide variant
Location: chr19:10356683 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.69 · 52 PDB
Residue 834: an α-helix; the protein kinase 1 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.Pro834Ser Uncertain significance ★ ⚠ same residue
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

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-pro834 (accessed [today's date]).

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