TJP3

tight junction protein 3, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 19:3708362-3750813

Links

ENSG00000105289 ∙ NCBI:27134 ∙ OMIM:612689 ∙ HGNC:11829 ∙ Uniprot:O95049 ∙ 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 TJP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TJP3 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				5	1	6
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	6	1

Variants in TJP3

This is a list of pathogenic ClinVar variants found in the TJP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3728675-T-C			Likely benign (Jun 01, 2022)
19-3730507-C-T			Benign (Aug 26, 2017)
19-3730627-C-T			Likely benign (Sep 01, 2022)
19-3739003-C-T			Likely benign (Jul 01, 2022)
19-3740705-C-T			Likely benign (Dec 01, 2022)
19-3746850-C-T			Likely benign (Sep 01, 2022)
19-3747877-C-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TJP3	protein_coding	protein_coding	ENST00000589378	21	42705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.71e-23	0.0214	125543	0	205	125748	0.000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.670	686	638	1.07	0.0000465	5930
Missense in Polyphen		258	255.31	1.0105		2417
Synonymous	0.0487	269	270	0.996	0.0000204	1929
Loss of Function	1.12	39	47.3	0.825	0.00000276	474

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00143	0.00140
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.00370	0.00365
Finnish	0.00128	0.00125
European (Non-Finnish)	0.000448	0.000431
Middle Eastern	0.00370	0.00365
South Asian	0.000594	0.000588
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: TJP1, TJP2, and TJP3 are closely related scaffolding proteins that link tight junction (TJ) transmembrane proteins such as claudins, junctional adhesion molecules, and occludin to the actin cytoskeleton (PubMed:16129888). The tight junction acts to limit movement of substances through the paracellular space and as a boundary between the compositionally distinct apical and basolateral plasma membrane domains of epithelial and endothelial cells. Binds and recruits PATJ to tight junctions where it connects and stabilizes apical and lateral components of tight junctions (PubMed:16129888). Promotes cell-cycle progression through the sequestration of cyclin D1 (CCND1) at tight junctions during mitosis which prevents CCND1 degradation during M-phase and enables S-phase transition (PubMed:21411630). With TJP1 and TJP2, participates to the junctional retention and stability of the transcription factor DBPA, but is not involved in its shuttling to the nucleus (By similarity). Contrary to TJP2, TJP3 is dispensable for individual viability, embryonic development, epithelial differentiation, and the establishment of TJs, at least in the laboratory environment (By similarity). {ECO:0000250|UniProtKB:O62683, ECO:0000250|UniProtKB:Q9QXY1, ECO:0000269|PubMed:16129888, ECO:0000269|PubMed:21411630}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.275
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.671

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tjp3
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: tjp3
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: increased curvature

Gene ontology

• Cellular component: nucleus;plasma membrane;bicellular tight junction
• Molecular function: protein binding