TEP1

telomerase associated protein 1, the group of WD repeat domain containing

Basic information

Region (hg38): 14:20365666-20413501

Links

ENSG00000129566 ∙ NCBI:7011 ∙ OMIM:601686 ∙ HGNC:11726 ∙ Uniprot:Q99973 ∙ 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 TEP1 gene.

• Inborn genetic diseases (134 variants)
• not provided (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEP1 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	4	7
missense			126	12	10	148
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	126	15	15

Variants in TEP1

This is a list of pathogenic ClinVar variants found in the TEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20368456-T-A		not specified	Uncertain significance (Dec 08, 2023)
14-20368478-C-T		not specified	Uncertain significance (Oct 30, 2023)
14-20368507-C-T		not specified	Uncertain significance (Sep 22, 2023)
14-20368542-G-A			Likely benign (Dec 01, 2022)
14-20368557-C-T			Benign (Apr 04, 2018)
14-20368812-G-T		not specified	Uncertain significance (May 16, 2023)
14-20368878-G-A		not specified	Uncertain significance (Nov 07, 2023)
14-20368894-C-T			Benign (Nov 20, 2018)
14-20369429-C-A		not specified	Uncertain significance (Dec 13, 2022)
14-20369465-G-A		not specified	Uncertain significance (Sep 19, 2022)
14-20369508-C-T		not specified	Uncertain significance (Oct 25, 2023)
14-20369542-G-C			Benign (Jul 15, 2020)
14-20369561-C-G		not specified	Uncertain significance (Nov 18, 2022)
14-20369576-T-C		not specified	Uncertain significance (Dec 28, 2023)
14-20369700-G-A		not specified	Uncertain significance (Jan 29, 2024)
14-20369718-G-A		not specified	Uncertain significance (Feb 10, 2022)
14-20371290-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-20371618-C-T		not specified	Uncertain significance (Jul 06, 2021)
14-20371622-T-C		not specified	Uncertain significance (Aug 04, 2023)
14-20372751-G-A		not specified	Uncertain significance (Jun 22, 2021)
14-20372761-G-A		not specified	Uncertain significance (Oct 26, 2022)
14-20372772-T-C			Likely benign (Oct 05, 2017)
14-20373037-C-T		not specified	Uncertain significance (Dec 12, 2023)
14-20373117-G-A		not specified	Uncertain significance (May 27, 2022)
14-20373125-A-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEP1	protein_coding	protein_coding	ENST00000262715	54	47763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.38e-49	0.411	125265	4	479	125748	0.00192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0789	1470	1.48e+3	0.994	0.0000875	16837
Missense in Polyphen		434	460.08	0.94331		5489
Synonymous	1.05	563	596	0.945	0.0000333	5546
Loss of Function	3.18	98	138	0.709	0.00000724	1485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00550	0.00543
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.00401	0.00354
Finnish	0.000187	0.000185
European (Non-Finnish)	0.00136	0.00135
Middle Eastern	0.00401	0.00354
South Asian	0.00399	0.00389
Other	0.00134	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini (PubMed:19179534). Also component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport (By similarity). Responsible for the localizing and stabilizing vault RNA (vRNA) association in the vault ribonucleoprotein particle. Binds to TERC (By similarity). {ECO:0000250|UniProtKB:P97499, ECO:0000269|PubMed:19179534}.
• Pathway: telomeres telomerase cellular aging and immortality (Consensus)

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.920
• rvis_EVS: 4.19
• rvis_percentile_EVS: 99.71

Haploinsufficiency Scores

• pHI: 0.210
• hipred: N
• hipred_score: 0.332
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.343

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tep1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; normal phenotype; skeleton phenotype

Gene ontology

• Biological process: telomere maintenance via recombination;RNA-dependent DNA biosynthetic process
• Cellular component: chromosome, telomeric region;telomerase holoenzyme complex;cytoplasm;nuclear matrix;ribonucleoprotein complex
• Molecular function: p53 binding;telomerase activity;RNA binding;ATP binding;enzyme binding;telomerase RNA binding