TEN1

TEN1 subunit of CST complex, the group of CST complex

Basic information

Region (hg38): 17:75979240-76000586

Previous symbols: [ "C17orf106" ]

Links

ENSG00000257949 ∙ NCBI:100134934 ∙ OMIM:613130 ∙ HGNC:37242 ∙ Uniprot:Q86WV5 ∙ 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 TEN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEN1 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					1	1
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2	1	1	4
Total	0	0	2	1	2

Variants in TEN1

This is a list of pathogenic ClinVar variants found in the TEN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75979246-G-A		Acyl-CoA oxidase deficiency	Uncertain significance (Jun 14, 2016)
17-75979259-A-T		Acyl-CoA oxidase deficiency	Uncertain significance (Jun 14, 2016)
17-75979390-C-T		Acyl-CoA oxidase deficiency	Benign/Likely benign (Sep 11, 2018)
17-75979728-C-T			Benign (Jul 27, 2021)
17-75986292-C-T			Benign (Jan 19, 2018)
17-75991577-G-A			Benign (Mar 02, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEN1	protein_coding	protein_coding	ENST00000397640	3	21367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0151	0.706	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.742	53	70.5	0.751	0.00000429	790
Missense in Polyphen		17	21.639	0.78563		242
Synonymous	-0.127	31	30.1	1.03	0.00000191	243
Loss of Function	0.654	3	4.50	0.667	1.91e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CST complex proposed to act as a specialized replication factor promoting DNA replication under conditions of replication stress or natural replication barriers such as the telomere duplex. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. Initially the CST complex has been proposed to protect telomeres from DNA degradation (PubMed:19854130). However, the CST complex has been shown to be involved in several aspects of telomere replication. The CST complex inhibits telomerase and is involved in telomere length homeostasis; it is proposed to bind to newly telomerase-synthesized 3' overhangs and to terminate telomerase action implicating the association with the ACD:POT1 complex thus interfering with its telomerase stimulation activity. The CST complex is also proposed to be involved in fill-in synthesis of the telomeric C-strand probably implicating recruitment and activation of DNA polymerase alpha (PubMed:22763445). The CST complex facilitates recovery from many forms of exogenous DNA damage; seems to be involved in the re-initiation of DNA replication at repaired forks and/or dormant origins (PubMed:25483097). {ECO:0000269|PubMed:19854130, ECO:0000269|PubMed:22763445, ECO:0000269|PubMed:25483097}.

Intolerance Scores

• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ten1

Gene ontology

• Biological process: telomere capping;negative regulation of telomere maintenance via telomerase;negative regulation of telomerase activity
• Cellular component: nuclear chromosome, telomeric region;nucleus;CST complex
• Molecular function: single-stranded DNA binding;protein binding;telomerase inhibitor activity;telomeric DNA binding