Is JAK3 p.Pro84= (c.252G>A) pathogenic?

JAK3 p.Pro84= (c.252G>A) is classified Conflicting classifications of pathogenicity in JAK3 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-02-01). Rare (popmax 0.243%, amr); Associated with T-B+ severe combined immunodeficiency due to JAK3 deficiency.

What condition is associated with JAK3 p.Pro84= (c.252G>A)?

JAK3 p.Pro84= (c.252G>A) is associated with T-B+ severe combined immunodeficiency due to JAK3 deficiency (ClinVar).

How common is JAK3 p.Pro84= (c.252G>A) in the general population?

JAK3 p.Pro84= (c.252G>A) is rare (popmax 0.243%, amr) (gnomAD).

JAK3 p.Pro84=

Q: How is T-B+ severe combined immunodeficiency due to JAK3 deficiency inherited?

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

c.252G>A · rs139738701 · VCV328520

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.243%, amr)

Conditions

T-B+ severe combined immunodeficiency due to JAK3 deficiency

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 -20	GERP -3.4
Overall
CADD	0.044	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.243% Admixed American · 146/60,000 alleles

Filtering AF 0.211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.199%

Overall 0.11% 1,772/1,613,336 alleles · rare exomes 1,614/1,461,286 · genomes 158/152,050 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.243%	411
European (non-Finnish)	0.127%	789
Remaining individualsnot grpmax-eligible	0.123%	812
Middle Eastern	0.0825%	1,212
African / African-American	0.0254%	3,945
South Asian	0.0209%	4,794
Finnishnot grpmax-eligible	0.0173%	5,770

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: JAK3
Protein: p.Pro84=
Coding: c.252G>A
MANE Select: NM_000215
dbSNP: rs139738701
Type: single nucleotide variant
Location: chr19:17843833 (GRCh38)
Gene constraint: LOEUF 0.933 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.20 · 43 PDB
Residue 84: the ferm domain; the 'interaction with cytokine/interferon/growth hormone receptors' region

Full JAK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

T-B+ severe combined immunodeficiency due to JAK3 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For T-B+ severe combined immunodeficiency due to JAK3 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

JAK3 p.Pro84Leu Uncertain significance ★ ⚠ same residue
JAK3 c.1701+1G>A Likely pathogenic ★★★ same condition
JAK3 c.2680+89G>A Likely pathogenic ★★★ same condition
JAK3 c.862-2A>G Likely pathogenic ★★★ same condition
JAK3 p.Arg350Trp Likely pathogenic ★★★ same condition
JAK3 p.Arg403His Likely pathogenic ★★★ ⚠ same condition
JAK3 p.Arg445Ter Pathogenic ★★★ same condition
JAK3 p.Arg451Ter Pathogenic ★★★ 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/jak3-p-pro84 (accessed [today's date]).

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