TJAP1

protein-coding

tight junction associated protein 1

Gene summary

This gene encodes a tight junction-associated protein. Incorporation of the encoded protein into tight junctions occurs at a late stage of formation of the junctions. The encoded protein localizes to the Golgi and may function in vesicle trafficking. Alternatively spliced transcript variants have been described. A related pseudogene exists on the X chromosome. [provided by RefSeq, Mar 2009]

Previous symbols:

TJP4

MANE transcript

NM_001350562.2

Inheritance

—

ClinVar variants

U:85B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr6:43,477,523-43,506,556

External References & Databases

Ensembl (ENSG00000137221)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TJAP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001350562.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			82 clinvar	1 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	85	3	0	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 210 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001350562.2	RefSeq	NP_001337491.1	8	MANE Select
ENST00000372449.6	Ensembl	ENSP00000361527.1	8	MANE Select
NM_001146016.2	RefSeq	NP_001139488.1	8	Standard
NM_001146017.2	RefSeq	NP_001139489.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tight junction - Homo sapiens (human)

Biological Process

Golgi organization

Molecular Function

protein binding

Cellular Component

endosome
Golgi apparatus
trans-Golgi network
plasma membrane
bicellular tight junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372445
Coding exons: 8
Length: 29034
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 125748
p: 0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.434	308	330	0.933	0.0000206	3576
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00047	0.00043	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00027	0.00026	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0400
RVIS EVS: 0.24
RVIS percentile EVS: 69.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.899

Gene Damage Prediction

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