Is TYK2 p.Arg679His (c.2036G>A) pathogenic?

TYK2 p.Arg679His (c.2036G>A) is classified Uncertain significance in TYK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-04). AlphaMissense: likely benign (0.0654); Ultra-rare (popmax 0.0167%, mid); Associated with immunodeficiency 35.

What condition is associated with TYK2 p.Arg679His (c.2036G>A)?

TYK2 p.Arg679His (c.2036G>A) is associated with immunodeficiency 35 (ClinVar).

How common is TYK2 p.Arg679His (c.2036G>A) in the general population?

TYK2 p.Arg679His (c.2036G>A) is ultra-rare (popmax 0.0167%, mid) (gnomAD).

What do computational predictors say about TYK2 p.Arg679His (c.2036G>A)?

AlphaMissense predicts likely benign (score 0.0654) — an in-silico prediction, not a clinical call.

TYK2 p.Arg679His

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.2036G>A · rs200247986 · VCV1411985

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0654 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0167%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

immunodeficiency 35

Computational evidence

Protein change
AlphaMissense	0.0654	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -8.89	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 1	GERP -2.1, phastCons 0.68
Regional constraint	o/e 0.86	unconstrained · MANE · 28 kb · p 6.7e-09 · regional, not allelic
Overall
CADD	16.75	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 0.0167% Middle Eastern · 1/5,992 alleles

Filtering AF 0.00613% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00565%

Overall 0.00628% 97/1,545,550 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0167%	5,992
European (non-Finnish)	0.00741%	13,492
South Asian	0.00595%	16,810
Remaining individualsnot grpmax-eligible	0.005%	20,019
Admixed American	0.00393%	25,463
African / African-American	0.00137%	72,910

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.Arg679His
Coding: c.2036G>A
MANE Select: NM_003331
dbSNP: rs200247986
Type: single nucleotide variant
Location: chr19:10361522 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.69 · 52 PDB
Residue 679: the protein kinase 1 domain; a β-strand

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.Arg679Cys Uncertain significance ★★ ⚠ same residue
TYK2 p.Arg679= Likely benign ★★ same residue
TYK2 p.Arg679Pro Conflicting classifications of pathogenicity ★ 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

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-arg679his (accessed [today's date]).

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