RTEL1-TNFRSF6B

RTEL1-TNFRSF6B readthrough (NMD candidate)

Basic information

Region (hg38): 20:63659300-63698684

Links

ENSG00000026036 ∙ NCBI:100533107 ∙ ∙ HGNC:44095 ∙ ∙ ∙ 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 RTEL1-TNFRSF6B gene.

• Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 (1475 variants)
• Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5 (723 variants)
• not provided (591 variants)
• Dyskeratosis congenita (421 variants)
• Inborn genetic diseases (209 variants)
• Dyskeratosis congenita, autosomal recessive 5 (199 variants)
• not specified (95 variants)
• Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 (52 variants)
• RTEL1-related condition (33 variants)
• Dyskeratosis congenita, autosomal dominant 1 (27 variants)
• Pulmonary fibrosis (18 variants)
• Interstitial lung disease 2 (11 variants)
• TNFRSF6B-related condition (8 variants)
• Telomere syndrome (3 variants)
• Dyskeratosis congenita, X-linked (2 variants)
• Microcephaly (2 variants)
• See cases (2 variants)
• Dyskeratosis congenita, autosomal dominant 4 (2 variants)
• Action myoclonus-renal failure syndrome (1 variants)
• Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (1 variants)
• Long QT syndrome (1 variants)
• RTEL1-related Disorders (1 variants)
• Immunodeficiency (1 variants)
• - (1 variants)
• Acute myeloid leukemia (1 variants)
• Abnormality of blood and blood-forming tissues (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTEL1-TNFRSF6B 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	10	49	105	164	5	333
splice region						0
non coding	66	65	1001	1208	121	2461
Total	76	114	1106	1372	126

Highest pathogenic variant AF is 0.0000723

Variants in RTEL1-TNFRSF6B

This is a list of pathogenic ClinVar variants found in the RTEL1-TNFRSF6B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63659310-C-T		not specified	Benign (Jan 24, 2024)
20-63659344-A-C			Benign (Feb 07, 2019)
20-63659394-C-G		not specified	Uncertain significance (Sep 27, 2019)
20-63659405-G-GCCCAAGATAGTCCTGAATGGTGTGACCGTAGACTTCCCTTTCC		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	Pathogenic (Apr 02, 2021)
20-63659407-C-A			Uncertain significance (Feb 01, 2024)
20-63659408-C-T		RTEL1-related disorder	Likely benign (Feb 23, 2022)
20-63659410-A-C		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5 • Dyskeratosis congenita	Uncertain significance (Sep 02, 2021)
20-63659410-AG-A		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	Pathogenic (Mar 29, 2021)
20-63659411-G-A		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	Likely benign (Dec 16, 2023)
20-63659414-A-C		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 • Dyskeratosis congenita • Inborn genetic diseases	Likely benign (Dec 30, 2023)
20-63659418-C-T		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Likely benign (Sep 11, 2023)
20-63659423-T-C		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Likely benign (May 30, 2023)
20-63659431-C-T		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Uncertain significance (Sep 01, 2021)
20-63659432-C-T		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 • Inborn genetic diseases	Likely benign (May 27, 2023)
20-63659433-G-A		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Uncertain significance (Nov 18, 2023)
20-63659438-C-T		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Likely benign (Sep 10, 2022)
20-63659444-T-C		not specified	Uncertain significance (Nov 21, 2017)
20-63659447-C-A		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 • Dyskeratosis congenita • RTEL1-related disorder	Uncertain significance (May 01, 2024)
20-63659448-C-T		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Pathogenic (Feb 26, 2021)
20-63659449-A-G		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	Uncertain significance (Jul 29, 2022)
20-63659451-C-T		Dyskeratosis congenita	Likely pathogenic (Oct 11, 2016)
20-63659453-C-T		Dyskeratosis congenita, autosomal recessive 5;Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	Likely benign (Aug 30, 2023)
20-63659456-C-T		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Likely benign (Jun 23, 2023)
20-63659457-A-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
20-63659458-A-G		Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3;Dyskeratosis congenita, autosomal recessive 5	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Gene ontology

• Biological process: DNA replication;DNA repair;DNA recombination;regulation of double-strand break repair via homologous recombination;DNA duplex unwinding;negative regulation of DNA recombination;telomeric loop disassembly;negative regulation of t-circle formation
• Cellular component: nucleus
• Molecular function: DNA binding;ATP-dependent DNA helicase activity;ATP binding;metal ion binding;4 iron, 4 sulfur cluster binding;DNA polymerase binding