JCHAIN

Chr 4

joining chain of multimeric IgA and IgM

Also known as: IGCJ, IGJ, JCH

NCBI Gene: 3512ENSG00000132465UniProt: P01591OMIM: 147790

The J chain protein links IgM and IgA immunoglobulin monomers to form pentameric IgM complexes and dimeric/polymeric IgA complexes, and facilitates binding to secretory component for mucosal immunity. Mutations cause immunodeficiency with absent serum IgM and decreased secretory IgA, resulting in recurrent infections particularly affecting respiratory and gastrointestinal tracts. This follows autosomal recessive inheritance.

OMIMResearchSummary from RefSeq, UniProt
GOFmechanismLOEUF 1.24
Clinical Summary— JCHAIN
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.03) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
21 unique Pathogenic / Likely Pathogenic· 20 VUS of 46 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.24LOEUF
pLI 0.034
Z-score 1.19
OE 0.48 (0.22–1.24)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.14Z-score
OE missense 0.96 (0.80–1.15)
84 obs / 87.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.48 (0.22–1.24)
0≤0.351.4
Missense OE0.96 (0.80–1.15)
0≤0.61.4
Synonymous OE0.73
0≤1.21.6
LoF obs/exp: 3 / 6.2Missense obs/exp: 84 / 87.7Syn Z: 1.21
DN
0.5181th %ile
GOF
0.6345th %ile
LOF
0.2775th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

46 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic20
Likely Pathogenic1
VUS20
Likely Benign3
20
Pathogenic
1
Likely Pathogenic
20
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
20
0
20
Likely Pathogenic
0
0
1
0
1
VUS
0
13
7
0
20
Likely Benign
0
1
0
2
3
Benign
0
0
0
0
0
Total01428244

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

JCHAIN · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients