TJAP1

tight junction associated protein 1

Basic information

Region (hg38): 6:43477523-43506556

Previous symbols: [ "TJP4" ]

Links

ENSG00000137221 ∙ NCBI:93643 ∙ OMIM:612658 ∙ HGNC:17949 ∙ Uniprot:Q5JTD0 ∙ 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 TJAP1 gene.

• not_specified (73 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TJAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001350562.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			73	1		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	76	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TJAP1	protein_coding	protein_coding	ENST00000372445	8	29034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000176	0.972	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.434	308	330	0.933	0.0000206	3576
Missense in Polyphen		117	134.22	0.87171		1472
Synonymous	0.224	125	128	0.975	0.00000690	1178
Loss of Function	2.00	11	20.9	0.527	0.00000116	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000781	0.000774
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000958	0.0000924
European (Non-Finnish)	0.000302	0.000299
Middle Eastern	0.000218	0.000217
South Asian	0.000267	0.000261
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.0400
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.51

Haploinsufficiency Scores

• pHI: 0.307
• hipred: N
• hipred_score: 0.285
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tjap1

Gene ontology

• Biological process: Golgi organization
• Cellular component: endosome;Golgi apparatus;trans-Golgi network;plasma membrane;bicellular tight junction
• Molecular function: protein binding