RTEL1 regulator of telomere elongation helicase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RTEL1provided by HGNC
Official Full Name: regulator of telomere elongation helicase 1provided by HGNC
Primary source: HGNC:HGNC:15888
See related: Ensembl:ENSG00000258366 MIM:608833; AllianceGenome:HGNC:15888
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NHL; RTEL; DKCA4; DKCB5; PFBMFT3; C20orf41
Summary: This gene encodes a DNA helicase which functions in the stability, protection and elongation of telomeres and interacts with proteins in the shelterin complex known to protect telomeres during DNA replication. Mutations in this gene have been associated with dyskeratosis congenita and Hoyerall-Hreidarsson syndrome. Read-through transcription of this gene into the neighboring downstream gene, which encodes tumor necrosis factor receptor superfamily, member 6b, generates a non-coding transcript. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
Expression: Ubiquitous expression in testis (RPKM 6.4), appendix (RPKM 4.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.33

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (63657810..63696253)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (65471931..65516559)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (62289163..62327606)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences.
Title: A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences.
Structural and biochemical characterization of the C-terminal region of the human RTEL1 helicase.
Title: Structural and biochemical characterization of the C-terminal region of the human RTEL1 helicase.
Exome sequencing in extreme altitude mountaineers identifies pathogenic variants in RTEL1 and COL6A1 previously associated with respiratory failure.
Title: Exome sequencing in extreme altitude mountaineers identifies pathogenic variants in RTEL1 and COL6A1 previously associated with respiratory failure.
High expression of RTEL1 predicates worse progression in gliomas and promotes tumorigenesis through JNK/ELK1 cascade.
Title: High expression of RTEL1 predicates worse progression in gliomas and promotes tumorigenesis through JNK/ELK1 cascade.
Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites.
Title: Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites.
RTEL1 gene polymorphisms and neuroblastoma risk in Chinese children.
Title: RTEL1 gene polymorphisms and neuroblastoma risk in Chinese children.
Human RTEL1 Interacts with KPNB1 (Importin beta) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase.
Title: Human RTEL1 Interacts with KPNB1 (Importin β) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase.
RTEL1 is upregulated in colorectal cancer and promotes tumor progression.
Title: RTEL1 is upregulated in colorectal cancer and promotes tumor progression.
Ultra-rare RTEL1 gene variants associate with acute severity of COVID-19 and evolution to pulmonary fibrosis as a specific long COVID disorder.
Title: Ultra-rare RTEL1 gene variants associate with acute severity of COVID-19 and evolution to pulmonary fibrosis as a specific long COVID disorder.
Regulator of telomere elongation helicase 1 gene and its association with malignancy.
Title: Regulator of telomere elongation helicase 1 gene and its association with malignancy.

Submit: New GeneRIF Correction See all GeneRIFs (71)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dyskeratosis congenita, autosomal recessive 5 MedGen: C3554656 OMIM: 615190 GeneReviews: Dyskeratosis Congenita and Related Telomere Biology Disorders	Compare labs
Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 MedGen: C4225346 OMIM: 616373 GeneReviews: Pulmonary Fibrosis Predisposition Overview, Dyskeratosis Congenita and Related Telomere Biology Disorders	Compare labs

EBI GWAS Catalog

Description
Chromosome 7p11.2 (EGFR) variation influences glioma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan of dental caries in the permanent dentition. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies five susceptibility loci for glioma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of glioma and meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Readthrough RTEL1-TNFRSF6B

Readthrough gene: RTEL1-TNFRSF6B, Included gene: TNFRSF6B

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 4 iron, 4 sulfur cluster binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables DNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA helicase activity	TAS Traceable Author Statement more info
enables DNA polymerase binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
enables isomerase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA duplex unwinding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA strand displacement	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA strand displacement	TAS Traceable Author Statement more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mitotic telomere maintenance via semi-conservative replication	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of DNA recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA recombination	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of t-circle formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of t-circle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of t-circle formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of t-circle formation	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of telomere maintenance in response to DNA damage	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of telomere capping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of telomere maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of telomere maintenance via telomere lengthening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of telomeric loop disassembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of double-strand break repair via homologous recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in replication fork processing	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in telomere maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance in response to DNA damage	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomeric loop disassembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomeric loop disassembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomeric loop disassembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromosome, telomeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear membrane	IDA Inferred from Direct Assay more info
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: regulator of telomere elongation helicase 1

Names: regulator of telomere length

NP_001269938.1

EC 3.6.4.12

NP_001269939.1

EC 3.6.4.12

NP_057518.1

EC 3.6.4.12

NP_116575.3

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033901.1 RefSeqGene

Range

5503..43436

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1149

mRNA and Protein(s)

NM_001283009.2 → NP_001269938.1 regulator of telomere elongation helicase 1 isoform 3

See identical proteins and their annotated locations for NP_001269938.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest protein (isoform 3).

Source sequence(s)

AF217795, AW005229, JX119186

Consensus CDS

CCDS63331.1

UniProtKB/TrEMBL

R4IXY3

Related

ENSP00000353332.5, ENST00000360203.11

Conserved Domains (3) summary

PRK07764
Location:989 → 1240

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd13932
Location:877 → 976

HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)

TIGR00604
Location:10 → 743

rad3; DNA repair helicase (rad3)
NM_001283010.1 → NP_001269939.1 regulator of telomere elongation helicase 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences, compared to variant 3. These differences include translation initiation at a downstream AUG and a translational frameshift. The resulting protein (isoform 4) has a shorter N-terminus and distinct C-terminus, compared to isoform 3.

Source sequence(s)

AF217795, AK304798, AW005229

Consensus CDS

CCDS74751.1

UniProtKB/Swiss-Prot

Q9NZ71

Related

ENSP00000322287.5, ENST00000318100.9

Conserved Domains (4) summary

cd13932
Location:654 → 753

HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)

TIGR00604
Location:2 → 520

rad3; DNA repair helicase (rad3)

pfam13307
Location:322 → 508

Helicase_C_2; Helicase C-terminal domain

cl21455
Location:1 → 49

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_016434.4 → NP_057518.1 regulator of telomere elongation helicase 1 isoform 1

See identical proteins and their annotated locations for NP_057518.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses an alternate splice site in the 3' coding region that results in a translational frameshift, compared to variant 3. The resulting protein (isoform 1) has a distinct C-terminus and is shorter than isoform 3.

Source sequence(s)

AF217795, AL353715

Consensus CDS

CCDS13531.1

UniProtKB/Swiss-Prot

A2A397, A2A398, B4DRM5, B4DYM3, B4E3N6, E1P5J4, E1P5J5, Q5JTV3, Q5JTV4, Q9BW37, Q9H402, Q9H4X6, Q9NX25, Q9NZ71, Q9NZ73, Q9UPR4, Q9Y4R6

UniProtKB/TrEMBL

R4IXY3

Related

ENSP00000359035.3, ENST00000370018.7

Conserved Domains (5) summary

cd13932
Location:877 → 976

HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)

TIGR00604
Location:10 → 743

rad3; DNA repair helicase (rad3)

pfam06733
Location:111 → 272

DEAD_2; DEAD_2

pfam13307
Location:545 → 731

Helicase_C_2; Helicase C-terminal domain

cl21455
Location:15 → 60

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_032957.5 → NP_116575.3 regulator of telomere elongation helicase 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 3, one of which results in a translational frameshift. The encoded protein (isoform 2) has a distinct C-terminus and is shorter than isoform 3.

Source sequence(s)

AF217795, AK302508, AL353715

Consensus CDS

CCDS13530.3

UniProtKB/TrEMBL

R4IXY3

Related

ENSP00000424307.2, ENST00000508582.7

Conserved Domains (5) summary

cd13932
Location:901 → 1000

HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)

TIGR00604
Location:10 → 767

rad3; DNA repair helicase (rad3)

pfam06733
Location:111 → 296

DEAD_2; DEAD_2

pfam13307
Location:569 → 755

Helicase_C_2; Helicase C-terminal domain

cl21455
Location:15 → 60

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

63657810..63696253

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

65471931..65516559

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_015647.2: Suppressed sequence

Description

NM_015647.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.