TEN1

gene
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Also known as FLJ39785

Summary

TEN1 (TEN1 subunit of CST complex, HGNC:37242) is a protein-coding gene on chromosome 17q25.1, encoding CST complex subunit TEN1 (Q86WV5). 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. It is a selective cancer dependency (DepMap: 57.0% of cell lines).

C17ORF106, or TEN1, appears to function in a telomere-associated complex with STN1 (OBFC1; MIM 613128) and CTC1 (C17ORF68; MIM 613129) (Miyake et al., 2009 [PubMed 19854130]).

Source: NCBI Gene 100134934 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 3 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 57.0% of screened cell lines
  • MANE Select transcript: NM_001113324

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:37242
Approved symbolTEN1
NameTEN1 subunit of CST complex
Location17q25.1
Locus typegene with protein product
StatusApproved
AliasesFLJ39785
Ensembl geneENSG00000257949
Ensembl biotypeprotein_coding
OMIM613130
Entrez100134934

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 retained_intron

ENST00000397640, ENST00000585710, ENST00000586891, ENST00000588202, ENST00000590676, ENST00000911175, ENST00000911176, ENST00000911177, ENST00000940414, ENST00000940415, ENST00000957727, ENST00000957728

RefSeq mRNA: 1 — MANE Select: NM_001113324 NM_001113324

CCDS: CCDS45780

Canonical transcript exons

ENST00000397640 — 4 exons

ExonStartEnd
ENSE000014041227597924075979511
ENSE000015294997600014176000586
ENSE000035077667599146675991623
ENSE000036050367598618775986284

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 93.08.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0086 / max 30.1615, expressed in 454 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
16281213.75891813
1628130.9583416
1628140.050411

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583493.08gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.73gold quality
skin of abdomenUBERON:000141691.68gold quality
skin of legUBERON:000151191.48gold quality
zone of skinUBERON:000001491.41gold quality
right lobe of liverUBERON:000111491.12gold quality
esophagus mucosaUBERON:000246990.76gold quality
apex of heartUBERON:000209890.48gold quality
mucosa of transverse colonUBERON:000499189.21gold quality
body of pancreasUBERON:000115088.47gold quality
right adrenal glandUBERON:000123388.47gold quality
body of stomachUBERON:000116188.07gold quality
right adrenal gland cortexUBERON:003582788.03gold quality
granulocyteCL:000009487.97gold quality
left adrenal gland cortexUBERON:003582587.82gold quality
minor salivary glandUBERON:000183087.77gold quality
duodenumUBERON:000211487.77gold quality
saliva-secreting glandUBERON:000104487.67gold quality
left adrenal glandUBERON:000123487.66gold quality
metanephros cortexUBERON:001053387.30gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.16gold quality
liverUBERON:000210787.13gold quality
monocyteCL:000057687.01gold quality
leukocyteCL:000073886.76gold quality
vaginaUBERON:000099686.55gold quality
olfactory segment of nasal mucosaUBERON:000538686.54gold quality
cortex of kidneyUBERON:000122586.53gold quality
pituitary glandUBERON:000000786.47gold quality
prostate glandUBERON:000236786.47gold quality
adult mammalian kidneyUBERON:000008286.44gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting TEN1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-185-3P99.9567.011743
HSA-MIR-466399.6265.33957
HSA-MIR-186-3P99.5166.241685
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-6804-5P98.3965.771084
HSA-MIR-4733-5P97.7567.44866
HSA-MIR-366597.7365.08975
HSA-MIR-6783-5P97.6767.211528

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 57.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 21)

  • Ctc1-Stn1-Ten1 is a replication protein A (RPA)-like complex that is not directly involved in conventional DNA replication at forks but plays a role in DNA metabolism frequently required by telomeres. (PMID:19854130)
  • the human CST (CTC1, STN1 and TEN1) complex, previously implicated in telomere protection and DNA metabolism, inhibits telomerase activity through primer sequestration and physical interaction with the protection of telomeres 1 (POT1)-TPP1 telomerase processivity factor (PMID:22763445)
  • data indicate that hTen1 is critical for the telomeric function of hCST, both in telomere protection and downregulation of telomerase function (PMID:23826127)
  • The mammalian CST (CTC1-STN1-TEN1) complex is directly involved at several stages of telomere end formation and CST seems to play critical roles in coordinating telomerase elongation and fill-in synthesis to complete telomere replication. (PMID:23851344)
  • TEN1 likely functions in conjunction with CTC1 and STN1 at the telomere and elsewhere in the genome. (PMID:24025336)
  • reveal a critical role for human Stn1 in telomere length maintenance and function, supporting the model that efficient replication of telomeric repeats is critical for long-term viability of normal somatic mammalian cells (PMID:25684230)
  • CTC1/STN1/TEN1 (CST) deficiency diminishes HU-induced RAD51 foci formation. (PMID:27487043)
  • TERT-mediated G-strand extension and Ctc1-Stn1-Ten1-mediated C-strand fill-in are equally important for telomere length maintenance. (PMID:28334750)
  • The findings imply that theCTC1/STN1/TEN1 complex(CST )complex plays an important role in regulating telomere maintenance in alternative-lengthening of telomeres(ALT) cells. (PMID:28366536)
  • Studies indicate telomere-binding proteins CTC1-STN1-TEN1 (CST) dysfunction and mutation is associated with several genetic diseases and cancers [Review]. (PMID:29293451)
  • CTC1-STN1 terminates TERT while STN1-TEN1 enables C-strand synthesis during telomere replication in colon cancer cells. (PMID:30026550)
  • The CST complex (CTC1-STN1-TEN1) maintains genome integrity through resolution of G4 structures both ahead of the replication fork and on the lagging strand template (PMID:30976812)
  • CST functions in two distinct aspects of genome-wide DNA replication, namely, origin licensing and replisome assembly. CST interacts with additional replisome components, MCM and AND-1. (PMID:30979824)
  • This work provides a blueprint to pinpoint the possible consequences of pathogenic mutations in the CST complex subunit TEN1. (PMID:31028137)
  • An Indian child with Coats plus syndrome due to mutations in STN1. (PMID:32627942)
  • Human CST complex protects stalled replication forks by directly blocking MRE11 degradation of nascent-strand DNA. (PMID:33210317)
  • CST in maintaining genome stability: Beyond telomeres. (PMID:33780718)
  • Pan-cancer analysis reveals that CTC1-STN1-TEN1 (CST) complex may have a key position in oncology. (PMID:35134616)
  • Structures of the human CST-Polalpha-primase complex bound to telomere templates. (PMID:35830881)
  • Reconstitution of a telomeric replicon organized by CST. (PMID:35831508)
  • CST-polymerase alpha-primase solves a second telomere end-replication problem. (PMID:38418884)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioten1ENSDARG00000097346
mus_musculusTen1ENSMUSG00000020778
rattus_norvegicusTen1ENSRNOG00000060307

Protein

Protein identifiers

CST complex subunit TEN1Q86WV5 (reviewed: Q86WV5)

Alternative names: Protein telomeric pathways with STN1 homolog, Telomere length regulation protein TEN1 homolog

All UniProt accessions (4): Q86WV5, K7EIL0, K7EJS2, K7EL09

UniProt curated annotations — full annotation on UniProt →

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. 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. 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.

Subunit / interactions. Component of the CST complex, composed of TEN1/C17orf106, CTC1/C17orf68 and STN1; in the complex interacts directly with STN1.

Subcellular location. Nucleus. Chromosome. Telomere.

Similarity. Belongs to the TEN1 family.

RefSeq proteins (1): NP_001106795* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012340NA-bd_OB-foldHomologous_superfamily
IPR029146Ten1_animal_plantFamily

Pfam: PF15490

UniProt features (15 total): strand 6, helix 3, mutagenesis site 2, chain 1, DNA-binding region 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
4JOIX-RAY DIFFRACTION2.05
6W6WELECTRON MICROSCOPY3
8D0BELECTRON MICROSCOPY3.43
8SOJELECTRON MICROSCOPY3.8
8SOKELECTRON MICROSCOPY4.1
8D0KELECTRON MICROSCOPY4.27
7U5CELECTRON MICROSCOPY4.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86WV5-F193.750.89

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

PositionPhenotype
1152.5-fold reduction in binding affinity for stn1.
1192-fold reduction in binding affinity for stn1.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-174411Polymerase switching on the C-strand of the telomere
R-HSA-174430Telomere C-strand synthesis initiation
R-HSA-157579Telomere Maintenance
R-HSA-1640170Cell Cycle
R-HSA-174417Telomere C-strand (Lagging Strand) Synthesis
R-HSA-180786Extension of Telomeres
R-HSA-73886Chromosome Maintenance

MSigDB gene sets: 98 (showing top): GOBP_RNA_TEMPLATED_DNA_BIOSYNTHETIC_PROCESS, GOBP_CHROMOSOME_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_TELOMERE_MAINTENANCE_VIA_TELOMERASE, GOBP_TELOMERE_CAPPING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_TELOMERE_MAINTENANCE_VIA_TELOMERE_LENGTHENING, GOBP_TELOMERE_ORGANIZATION, CHANDRAN_METASTASIS_DN, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_REGULATION_OF_TELOMERE_MAINTENANCE, GOBP_NEGATIVE_REGULATION_OF_DNA_BIOSYNTHETIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_TELOMERE_MAINTENANCE_VIA_TELOMERE_LENGTHENING, GOBP_NEGATIVE_REGULATION_OF_CHROMOSOME_ORGANIZATION, GOBP_DNA_BIOSYNTHETIC_PROCESS, REACTOME_EXTENSION_OF_TELOMERES

GO Biological Process (2): telomere capping (GO:0016233), negative regulation of telomere maintenance via telomerase (GO:0032211)

GO Molecular Function (5): single-stranded DNA binding (GO:0003697), telomerase inhibitor activity (GO:0010521), telomeric repeat DNA binding (GO:0042162), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): chromosome, telomeric region (GO:0000781), nucleus (GO:0005634), nucleoplasm (GO:0005654), CST complex (GO:1990879), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Telomere C-strand (Lagging Strand) Synthesis2
Chromosome Maintenance1
Extension of Telomeres1
Telomere Maintenance1
Cell Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
telomere maintenance1
telomere maintenance via telomerase1
regulation of telomere maintenance via telomerase1
negative regulation of telomere maintenance via telomere lengthening1
negative regulation of DNA biosynthetic process1
DNA binding1
telomerase activity1
enzyme inhibitor activity1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosomal region1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
nuclear telomere cap complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

286 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TEN1CTC1Q2NKJ3994
TEN1STN1Q9H668986
TEN1ANKRD10Q9NXR5545
TEN1RIF1Q5UIP0509
TEN1SHLD2Q86V20493
TEN1C1orf226A1L170475
TEN1SHLD3Q6ZNX1455
TEN1SHLD1Q8IYI0419
TEN1TINF2Q9BSI4379
TEN1CDYL2Q8N8U2353
TEN1DHRS1Q96LJ7351
TEN1DDX47Q9H0S4349
TEN1SNRNP25Q9BV90348
TEN1ACDQ96AP0348
TEN1MGRN1O60291347

IntAct

87 interactions, top by confidence:

ABTypeScore
TEN1STN1psi-mi:“MI:0915”(physical association)0.910
STN1TEN1psi-mi:“MI:0915”(physical association)0.910
TEN1CTC1psi-mi:“MI:0915”(physical association)0.860
CTC1TEN1psi-mi:“MI:0915”(physical association)0.860
TEN1CTC1psi-mi:“MI:0914”(association)0.860
CTC1TEN1psi-mi:“MI:0914”(association)0.860
TEN1CASP6psi-mi:“MI:0915”(physical association)0.560
TEN1FGFR3psi-mi:“MI:0915”(physical association)0.560
GRIN2CTEN1psi-mi:“MI:0915”(physical association)0.560
TEN1HSPB1psi-mi:“MI:0915”(physical association)0.560
TEN1LAMP2psi-mi:“MI:0915”(physical association)0.560
TEN1PRPHpsi-mi:“MI:0915”(physical association)0.560
TEN1PRPS1psi-mi:“MI:0915”(physical association)0.560
TEN1RANpsi-mi:“MI:0915”(physical association)0.560
TEN1psi-mi:“MI:0915”(physical association)0.560
TEN1BAG6psi-mi:“MI:0915”(physical association)0.560
KLF11TEN1psi-mi:“MI:0915”(physical association)0.560
TEN1NUP58psi-mi:“MI:0915”(physical association)0.560
TEN1KIF1Bpsi-mi:“MI:0915”(physical association)0.560
TEN1HTRA2psi-mi:“MI:0915”(physical association)0.560
TEN1UBQLN1psi-mi:“MI:0915”(physical association)0.560
TEN1PRPF40Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (18): TEN1 (Affinity Capture-MS), TEN1 (Affinity Capture-MS), CTC1 (Affinity Capture-MS), TEN1 (Two-hybrid), TEN1 (Affinity Capture-RNA), CTC1 (Affinity Capture-MS), TPR (Affinity Capture-MS), TEN1 (Affinity Capture-MS), YTHDC2 (Affinity Capture-MS), TEN1 (Co-fractionation), TEN1 (Co-fractionation), TEN1 (Co-fractionation), TEN1 (Co-fractionation), TEN1 (Co-fractionation), TEN1 (Affinity Capture-Western)

ESM2 similar proteins: A0JNQ6, A2RT67, A2RUS2, A6NC42, A6NGQ2, A9X185, O75031, O75817, O94955, O95267, P50747, Q06VW1, Q0II25, Q0ZFW8, Q1RMS8, Q1RMZ1, Q29108, Q2TBA3, Q3T0J1, Q3TYS2, Q4VX76, Q568D5, Q568M3, Q587J7, Q5JSQ8, Q5T9G4, Q5ZLS2, Q62522, Q69ZK0, Q6AYA6, Q6P5G6, Q7Z7H3, Q80X86, Q86WV5, Q8BXK4, Q8C0Q9, Q8CHQ0, Q8TCU6, Q8WUE5, Q91Z62

Diamond homologs: Q86WV5, Q9D7K2

SIGNOR signaling

1 interactions.

AEffectBMechanism
TEN1“form complex”“CST complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

3 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3243044NC_000017.10:g.(?73974677)(73976617_?)delPathogenic

SpliceAI

531 predictions. Top by Δscore:

VariantEffectΔscore
17:75991460:TTCCA:Tacceptor_loss1.0000
17:75991461:TCCA:Tacceptor_loss1.0000
17:75991463:CA:Cacceptor_loss1.0000
17:75991465:G:GAacceptor_loss1.0000
17:75991619:GCAGG:Gdonor_gain1.0000
17:75991622:GG:Gdonor_gain1.0000
17:75991623:GG:Gdonor_gain1.0000
17:75979508:ACAGG:Adonor_loss0.9900
17:75979509:CAGG:Cdonor_loss0.9900
17:75979510:AGGTT:Adonor_loss0.9900
17:75991464:A:AGacceptor_gain0.9900
17:75991465:G:GGacceptor_gain0.9900
17:75991465:GGT:Gacceptor_gain0.9900
17:75991465:GGTT:Gacceptor_gain0.9900
17:75991621:AGG:Adonor_loss0.9900
17:75991624:G:GGdonor_gain0.9900
17:75991625:T:Gdonor_loss0.9900
17:76000139:A:AGacceptor_gain0.9900
17:76000140:G:GGacceptor_gain0.9900
17:75986183:ACAG:Aacceptor_loss0.9800
17:75986184:C:Gacceptor_loss0.9800
17:75986185:A:Tacceptor_loss0.9800
17:75991464:AG:Aacceptor_gain0.9800
17:75991464:AGGTT:Aacceptor_gain0.9800
17:75991465:GG:Gacceptor_gain0.9800
17:75991465:GGTTG:Gacceptor_gain0.9800
17:76000140:GAC:Gacceptor_gain0.9800
17:76000140:GACA:Gacceptor_gain0.9800
17:75986132:A:AGacceptor_gain0.9700
17:75986133:G:GGacceptor_gain0.9700

AlphaMissense

794 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:75986281:G:AG30D0.977
17:75991597:T:AV75D0.971
17:75991602:G:TG77W0.971
17:75986273:A:CR27S0.968
17:75986273:A:TR27S0.968
17:75986280:G:CG30R0.967
17:75991543:T:AV57D0.963
17:75986281:G:TG30V0.961
17:75991549:C:TT59I0.961
17:75991602:G:AG77R0.960
17:75991602:G:CG77R0.960
17:75991603:G:TG77V0.959
17:75991603:G:AG77E0.958
17:75991590:T:GY73D0.949
17:75991504:T:AL44Q0.948
17:75986229:T:AW13R0.944
17:75986229:T:CW13R0.944
17:75986275:C:AT28K0.943
17:75986277:T:CF29L0.943
17:75986279:T:AF29L0.943
17:75986279:T:GF29L0.943
17:75991468:T:CL32S0.941
17:75986272:G:CR27T0.936
17:76000162:C:AA91E0.936
17:76000204:T:CL105S0.933
17:76000212:G:CA108P0.931
17:75991504:T:GL44R0.929
17:75986231:G:CW13C0.925
17:75986231:G:TW13C0.925
17:76000165:G:CR92P0.921

dbSNP variants (sampled 300 via entrez): RS1000059064 (17:75977297 G>A,C), RS1000082215 (17:75984173 G>A,C), RS1000606997 (17:76000518 C>A,T), RS1000672697 (17:75988618 A>C,G), RS1000721935 (17:75994905 G>A), RS1000735619 (17:75990693 G>A,T), RS1000768201 (17:75996147 T>C), RS1000799225 (17:75995880 C>A,T), RS1001041525 (17:75988913 G>T), RS1001069172 (17:75989049 G>A), RS1001081127 (17:75982585 CTTTGT>C,CTTTGTTTTGT), RS1001135066 (17:75982277 T>G), RS1001280873 (17:75995993 G>A), RS1001290573 (17:75995723 A>G), RS1001353626 (17:75988794 C>T)

Disease associations

OMIM: gene MIM:613130 | disease phenotypes: MIM:264470

GenCC curated gene-disease

Mondo (1): peroxisomal acyl-CoA oxidase deficiency (MONDO:0009919)

Orphanet (1): Peroxisomal acyl-CoA oxidase deficiency (Orphanet:2971)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010107_21L-selectin levels7.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008202L-Selectin measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C536662Peroxisomal ACYL-COA oxidase deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects expression2
bisphenol Aincreases expression1
beta-lapachonedecreases expression1
perfluorooctanoic acidaffects cotreatment, increases expression1
abrineincreases expression1
Cadmiumincreases expression, increases abundance1
Cosmeticsaffects cotreatment, increases expression1
Flame Retardantsincreases expression, affects cotreatment1
Plasticizersincreases expression, affects cotreatment1
Smokedecreases expression1
Urethaneincreases expression1
Antirheumatic Agentsdecreases expression1
Cadmium Chlorideincreases abundance, increases expression1
Phytoestrogensaffects cotreatment, increases expression1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01668186Not specifiedRECRUITINGLongitudinal Natural History Study of Patients With Peroxisome Biogenesis Disorders (PBD)
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): peroxisomal acyl-CoA oxidase deficiency