JCHAIN
protein-codingjoining chain of multimeric IgA and IgM
Gene summary
Enables IgA binding activity and protein homodimerization activity. Contributes to several functions, including immunoglobulin receptor binding activity; peptidoglycan binding activity; and phosphatidylcholine binding activity. Involved in several processes, including glomerular filtration; innate immune response; and positive regulation of respiratory burst. Located in obsolete extracellular space. Part of monomeric IgA immunoglobulin complex; pentameric IgM immunoglobulin complex; and secretory dimeric IgA immunoglobulin complex. [provided by Alliance of Genome Resources, Jun 2026]
- IGJ
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JCHAIN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144646.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 14 | 1 | 15 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 14 | 3 | 0 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653247.1 | 4 | MANE Select | |
| Ensembl | ENSP00000254801.4 | 4 | MANE Select | |
| Ensembl | ENSP00000426045.1 | 5 | Standard | |
| Ensembl | ENSP00000417560.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell surface interactions at the vascular wall
- Hemostasis
Biological Process
- retina homeostasis
- adaptive immune response
- glomerular filtration
- receptor-mediated endocytosis
- immune response
Molecular Function
- single-stranded DNA binding
- antigen binding
- IgA binding
- protein binding, bridging
- phosphatidylcholine binding
Cellular Component
- extracellular region
- extracellular space
- extracellular exosome
- monomeric IgA immunoglobulin complex
- dimeric IgA immunoglobulin complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254801
- Coding exons
- 4
- Length
- 26277
- Individuals with no LoFs
- 125617
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125626
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.140 | 84 | 87.7 | 0.958 | 0.00000430 | 1050 |
| Missense (PolyPhen) | 21 | 25.011 | 0.83962 | 336 | ||
| Synonymous | 1.21 | 23 | 31.6 | 0.727 | 0.00000160 | 298 |
| Loss of Function | 1.19 | 3 | 6.21 | 0.483 | 3.47e-7 | 72 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Serves to link two monomer units of either IgM or IgA. In the case of IgM, the J chain-joined dimer is a nucleating unit for the IgM pentamer, and in the case of IgA it induces larger polymers. It also help to bind these immunoglobulins to secretory component. {ECO:0000250|UniProtKB:P01592}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.54
Essentials
- Essential (gene trap)
- N