JCHAIN

joining chain of multimeric IgA and IgM

Basic information

Region (hg38): 4:70655541-70681817

Previous symbols: [ "IGJ" ]

Links

ENSG00000132465 ∙ NCBI:3512 ∙ OMIM:147790 ∙ HGNC:5713 ∙ Uniprot:P01591 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JCHAIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JCHAIN gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in JCHAIN

This is a list of pathogenic ClinVar variants found in the JCHAIN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-70656514-C-G		not specified	Uncertain significance (Jan 03, 2024)
4-70662165-G-A		not specified	Uncertain significance (Sep 30, 2022)
4-70662172-C-A		not specified	Uncertain significance (Jun 11, 2024)
4-70666483-T-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JCHAIN	protein_coding	protein_coding	ENST00000254801	4	26277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0338	0.835	125617	0	9	125626	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.140	84	87.7	0.958	0.00000430	1050
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000528
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.0632
• hipred: N
• hipred_score: 0.144
• ghis: 0.525

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jchain
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: retina homeostasis;adaptive immune response;glomerular filtration;receptor-mediated endocytosis;immune response;antibacterial humoral response;positive regulation of protein oligomerization;innate immune response;leukocyte migration;positive regulation of respiratory burst
• Cellular component: extracellular region;extracellular space;extracellular exosome;monomeric IgA immunoglobulin complex;dimeric IgA immunoglobulin complex;secretory IgA immunoglobulin complex;secretory dimeric IgA immunoglobulin complex;pentameric IgM immunoglobulin complex;hexameric IgM immunoglobulin complex;blood microparticle
• Molecular function: single-stranded DNA binding;antigen binding;IgA binding;protein binding, bridging;phosphatidylcholine binding;immunoglobulin receptor binding;protein homodimerization activity;peptidoglycan binding