Is TYK2 p.Pro853Arg (c.2558C>G) pathogenic?

TYK2 p.Pro853Arg (c.2558C>G) is classified Uncertain significance in TYK2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-07-18). AlphaMissense: likely benign (0.1751); Rare (popmax 0.196%, sas); Associated with immunodeficiency 35.

What condition is associated with TYK2 p.Pro853Arg (c.2558C>G)?

TYK2 p.Pro853Arg (c.2558C>G) is associated with immunodeficiency 35 (ClinVar).

How common is TYK2 p.Pro853Arg (c.2558C>G) in the general population?

TYK2 p.Pro853Arg (c.2558C>G) is rare (popmax 0.196%, sas) (gnomAD).

What do computational predictors say about TYK2 p.Pro853Arg (c.2558C>G)?

AlphaMissense predicts likely benign (score 0.1751) — an in-silico prediction, not a clinical call.

TYK2 p.Pro853Arg

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.2558C>G · rs551747806 · VCV891975

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1751 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.196%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

immunodeficiency 35

Computational evidence

Protein change
AlphaMissense	0.1751	likely benign
REVEL	0.433	indeterminate
SaProt	LLR -10.67	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP -0.51, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 28 kb · p 6.7e-09 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.196% South Asian · 178/91,014 alleles

Filtering AF 0.172% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.163%

Overall 0.0115% 186/1,613,746 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.196%	511
Middle Eastern	0.0336%	2,976
Remaining individualsnot grpmax-eligible	0.008%	12,496
European (non-Finnish)	8.47e-05%	1,179,942

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.Pro853Arg
Coding: c.2558C>G
MANE Select: NM_003331
dbSNP: rs551747806
Type: single nucleotide variant
Location: chr19:10356627 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.69 · 52 PDB
Residue 853: 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.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-pro853arg (accessed [today's date]).

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