TEPSIN
protein-codingTEPSIN adaptor related protein complex 4 accessory protein
Gene summary
Located in coated vesicle membrane and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C17orf56
- ENTHD2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.8 kbGenCC 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 TEPSIN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001363764.2. 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 | 3 | 1 | 4 | |||
| missense | 11 | 3 | 2 | 16 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 12 | 6 | 3 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001350693.1 | 13 | MANE Select | |
| Ensembl | ENSP00000490393.1 | 13 | MANE Select | |
| RefSeq | NP_653280.1 | 12 | Standard | |
| Ensembl | ENSP00000300714.3 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- cytoplasm
- Golgi apparatus
- cytosol
- nuclear speck
- AP-4 adaptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000300714
- Coding exons
- 12
- Length
- 10815
- Individuals with no LoFs
- 125670
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 14
- Defined
- 125685
- p
- 0.0000597
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0800 | 317 | 313 | 1.01 | 0.0000206 | 3288 |
| Missense (PolyPhen) | 73 | 78.329 | 0.93196 | 900 | ||
| Synonymous | -0.657 | 155 | 145 | 1.07 | 0.0000107 | 1112 |
| Loss of Function | 0.691 | 14 | 17.1 | 0.820 | 8.26e-7 | 199 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000083 | 0.000079 | rare |
| South Asian | 0.00011 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Associates with the adapter-like complex 4 (AP-4) and may therefore play a role in vesicular trafficking of proteins at the trans-Golgi network. {ECO:0000305|PubMed:22472443, ECO:0000305|PubMed:26542808}.;
Recessive Scores
- pRec
- 0.0890
Intolerance Scores
- RVIS EVS
- 0.62
- RVIS percentile EVS
- 83.53
Essentials
- Essential (gene trap)
- N