TEP1

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

Basic information

Region (hg38): 14:20365667-20413501

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.

not_specified (385 variants)
not_provided (25 variants)
TEP1-related_condition (1 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. These statistics are base on transcript: NM_000007110.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	4 clinvar	9
missense			359 clinvar	30 clinvar	7 clinvar	396
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	360	35	11

Loading clinvar variants...

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