JAML

junction adhesion molecule like, the group of V-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 11:118193725-118225092

Previous symbols: [ "AMICA1" ]

Links

ENSG00000160593 ∙ NCBI:120425 ∙ OMIM:609770 ∙ HGNC:19084 ∙ Uniprot:Q86YT9 ∙ 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 JAML gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JAML 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in JAML

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

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

Position	Type	Phenotype	Significance	ClinVar
11-118200493-T-G		not specified	Uncertain significance (Sep 27, 2021)
11-118203560-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-118203614-A-T		not specified	Uncertain significance (Sep 27, 2021)
11-118212412-C-T		not specified	Uncertain significance (Jul 06, 2021)
11-118212552-A-G		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JAML	protein_coding	protein_coding	ENST00000356289	9	31355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000747	0.983	125455	0	293	125748	0.00117

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.340	211	225	0.936	0.0000124	2566
Missense in Polyphen		49	58.414	0.83883		704
Synonymous	0.214	83	85.5	0.971	0.00000473	782
Loss of Function	2.12	8	17.6	0.454	8.08e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00266	0.00266
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00171	0.00171
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transmembrane protein of the plasma membrane of leukocytes that control their migration and activation through interaction with CXADR, a plasma membrane receptor found on adjacent epithelial and endothelial cells. The interaction between both receptors mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. Upon epithelial CXADR-binding, JAML induces downstream cell signaling events in gamma-delta T-cells through PI3-kinase and MAP kinases. It results in proliferation and production of cytokines and growth factors by T-cells that in turn stimulate epithelial tissues repair. It also controls the transmigration of leukocytes within epithelial and endothelial tissues through adhesive interactions with epithelial and endothelial CXADR. {ECO:0000269|PubMed:12869515, ECO:0000269|PubMed:15800062, ECO:0000269|PubMed:18948633, ECO:0000269|PubMed:19064666}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.0335
• hipred: N
• hipred_score: 0.179
• ghis: 0.447

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jaml

Gene ontology

• Biological process: heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;neutrophil chemotaxis;monocyte extravasation;gamma-delta T cell activation;regulation of immune response;leukocyte migration;positive regulation of epithelial cell proliferation involved in wound healing;neutrophil extravasation
• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane
• Molecular function: integrin binding;protein homodimerization activity;cell adhesion molecule binding