TEPSIN

TEPSIN adaptor related protein complex 4 accessory protein

Basic information

Region (hg38): 17:81228277-81239091

Previous symbols: [ "C17orf56", "ENTHD2" ]

Links

ENSG00000167302 ∙ NCBI:146705 ∙ ∙ HGNC:26458 ∙ Uniprot:Q96N21 ∙ 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 TEPSIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEPSIN 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				3	1	4
missense			8	2	2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	5	3

Variants in TEPSIN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-81228943-C-T			Benign (May 21, 2018)
17-81228969-G-C		not specified	Uncertain significance (Nov 15, 2021)
17-81229023-C-G		not specified	Uncertain significance (Jul 26, 2021)
17-81229039-C-T			Likely benign (May 01, 2022)
17-81229040-G-A		not specified	Uncertain significance (Nov 08, 2021)
17-81229041-C-T			Benign (May 21, 2018)
17-81229127-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-81229148-G-T			Benign (May 21, 2018)
17-81229301-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-81229313-G-A		not specified	Likely benign (Jun 11, 2021)
17-81231605-C-T		not specified	Uncertain significance (Aug 17, 2021)
17-81231865-G-A		not specified	Uncertain significance (Jul 08, 2021)
17-81231912-C-T			Likely benign (May 01, 2023)
17-81231968-C-T		not specified	Likely benign (Aug 17, 2021)
17-81232361-G-A			Likely benign (Apr 01, 2022)
17-81233995-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEPSIN	protein_coding	protein_coding	ENST00000300714	12	10815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.82e-9	0.314	125670	1	14	125685	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0800	317	313	1.01	0.0000206	3288
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000831	0.0000792
Middle Eastern	0.000165	0.000163
South Asian	0.000112	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.0916
• hipred: N
• hipred_score: 0.146
• ghis: 0.508

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tepsin

Gene ontology

• Cellular component: cytoplasm;Golgi apparatus;cytosol;nuclear speck;AP-4 adaptor complex;coated vesicle membrane;extrinsic component of organelle membrane;nuclear membrane;trans-Golgi network membrane
• Molecular function: protein binding