JAM2

junctional adhesion molecule 2, the group of V-set domain containing|CD molecules|Ig-like cell adhesion molecule family|I-set domain containing

Basic information

Region (hg38): 21:25639257-25717562

Previous symbols: [ "C21orf43" ]

Links

ENSG00000154721 ∙ NCBI:58494 ∙ OMIM:606870 ∙ HGNC:14686 ∙ Uniprot:P57087 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• basal ganglia calcification, idiopathic, 8, autosomal recessive (Strong), mode of inheritance: AR
• basal ganglia calcification, idiopathic, 8, autosomal recessive (Strong), mode of inheritance: AR
• bilateral striopallidodentate calcinosis (Supportive), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 8, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Basal ganglia calcification, idiopathic, 8, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	31851307; 32142645

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JAM2 gene.

• not provided (1 variants)
• JAM2-related disorder (1 variants)
• Basal ganglia calcification, idiopathic, 8, autosomal recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JAM2 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				1	2	3
missense			17		2	19
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					17	17
Total	1	0	17	1	21

Highest pathogenic variant AF is 0.0000197

Variants in JAM2

This is a list of pathogenic ClinVar variants found in the JAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-25639776-C-A			Benign (May 12, 2021)
21-25639822-A-G		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 27, 2020)
21-25639842-C-A			Benign (May 04, 2021)
21-25639886-G-A		Inborn genetic diseases	Uncertain significance (Feb 01, 2023)
21-25683787-C-A			Benign (May 12, 2021)
21-25683934-C-T		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
21-25683938-A-G			Benign (May 04, 2021)
21-25689871-AT-A		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 27, 2020)
21-25689908-CCAGA-C		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 27, 2020)
21-25693548-T-C			Benign (May 12, 2021)
21-25693607-A-G			Benign (May 13, 2021)
21-25693777-A-C		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
21-25693837-G-A		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 27, 2020)
21-25693837-G-T		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
21-25698675-A-AG		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 27, 2020)
21-25698693-A-G			Benign (May 09, 2021)
21-25698706-C-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
21-25698757-G-C		Inborn genetic diseases	Uncertain significance (May 11, 2022)
21-25698786-G-C		Basal ganglia calcification, idiopathic, 8, autosomal recessive	Pathogenic (Mar 30, 2020)
21-25698800-T-C		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
21-25698803-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
21-25698854-C-T		Inborn genetic diseases	Uncertain significance (Apr 19, 2024)
21-25702178-T-C			Likely benign (May 01, 2022)
21-25702222-G-A		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
21-25702224-A-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JAM2	protein_coding	protein_coding	ENST00000400532	10	78291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00615	0.990	124768	0	29	124797	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	127	166	0.764	0.00000880	1981
Missense in Polyphen		26	45.846	0.56712		567
Synonymous	1.95	42	61.4	0.684	0.00000323	623
Loss of Function	2.53	7	18.8	0.372	0.00000106	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000410
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000628	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000147	0.000141
Middle Eastern	0.0000628	0.0000556
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the processes of lymphocyte homing to secondary lymphoid organs.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Integrin cell surface interactions;Extracellular matrix organization;Cell surface interactions at the vascular wall;Hemostasis;Beta1 integrin cell surface interactions;amb2 Integrin signaling;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.466
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Jam2
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; normal 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; skeleton phenotype; immune system phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: jam2a
• Affected structure: fast muscle cell
• Phenotype tag: abnormal
• Phenotype quality: mononucleate

Gene ontology

• Biological process: negative regulation of cell adhesion;extracellular matrix organization;leukocyte migration;cell-cell adhesion
• Cellular component: plasma membrane;integral component of plasma membrane;bicellular tight junction
• Molecular function: protein binding;protein heterodimerization activity