TERF1

telomeric repeat binding factor 1, the group of Shelterin complex|Myb/SANT domain containing

Basic information

Region (hg38): 8:73008855-73048123

Previous symbols: [ "TRBF1" ]

Links

ENSG00000147601 ∙ NCBI:7013 ∙ OMIM:600951 ∙ HGNC:11728 ∙ Uniprot:P54274 ∙ 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 TERF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TERF1 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				3	3	6
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					17	17
Total	0	0	15	4	20

Variants in TERF1

This is a list of pathogenic ClinVar variants found in the TERF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-73008928-C-T		TERF1-related disorder	Likely benign (Aug 14, 2019)
8-73008941-A-G		not specified	Uncertain significance (Oct 10, 2023)
8-73008948-C-T		not specified	Uncertain significance (Sep 16, 2021)
8-73008962-G-A		not specified	Uncertain significance (Dec 11, 2023)
8-73009171-C-T			Benign (Jun 15, 2019)
8-73009188-C-T		not specified	Uncertain significance (Oct 30, 2023)
8-73009299-G-GGAGGTCGGGAGA			Benign (Jun 15, 2019)
8-73013904-A-C		not specified	Uncertain significance (Aug 17, 2022)
8-73013924-G-C		not specified	Uncertain significance (Aug 12, 2021)
8-73013948-A-G		not specified	Uncertain significance (Apr 07, 2023)
8-73014001-T-G			Benign (Jun 14, 2019)
8-73014208-C-T			Benign (Jun 15, 2019)
8-73020753-A-G		not specified	Uncertain significance (Jul 09, 2021)
8-73021004-T-C			Benign (Jun 14, 2019)
8-73024898-A-G		not specified	Uncertain significance (Aug 04, 2023)
8-73024941-A-G		TERF1-related disorder	Likely benign (May 24, 2019)
8-73026642-T-A			Benign (Aug 15, 2019)
8-73026726-T-G			Benign (Jun 21, 2019)
8-73026900-A-G			Benign (Jun 21, 2019)
8-73027121-G-A			Benign (Jun 21, 2019)
8-73027123-C-T			Benign (Jun 21, 2019)
8-73030122-A-C			Benign (Jun 15, 2019)
8-73030477-C-T			Benign (Jun 14, 2019)
8-73030587-G-C			Benign (Jun 15, 2019)
8-73032074-A-C		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TERF1	protein_coding	protein_coding	ENST00000276603	10	39259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.907	0.0934	125712	0	14	125726	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	202	217	0.929	0.0000101	2905
Missense in Polyphen		43	68.424	0.62843		937
Synonymous	-1.49	92	75.5	1.22	0.00000376	761
Loss of Function	3.62	3	20.9	0.144	9.71e-7	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000100	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000830	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000722	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and negatively regulates telomere length. Involved in the regulation of the mitotic spindle. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double- stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. {ECO:0000269|PubMed:16166375}.
• Pathway: telomeres telomerase cellular aging and immortality;Packaging Of Telomere Ends;Telomere Maintenance;Chromosome Maintenance;Cell Cycle;Regulation of Telomerase (Consensus)

Recessive Scores

• pRec: 0.281

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.536
• hipred: Y
• hipred_score: 0.743
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.687

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Terf1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; immune system phenotype; digestive/alimentary phenotype; pigmentation phenotype; neoplasm; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: telomere maintenance;regulation of transcription by RNA polymerase II;telomere maintenance via telomerase;negative regulation of DNA replication;telomere capping;negative regulation of telomere maintenance via telomerase;negative regulation of telomere maintenance via semi-conservative replication;response to drug;meiotic telomere clustering;cell division;negative regulation of telomerase activity;telomeric D-loop disassembly;t-circle formation;negative regulation of telomere maintenance via telomere lengthening;positive regulation of shelterin complex assembly;negative regulation of establishment of protein localization to telomere;negative regulation of establishment of RNA localization to telomere;negative regulation of establishment of protein-containing complex localization to telomere;negative regulation of exonuclease activity;negative regulation of telomeric D-loop disassembly
• Cellular component: nuclear telomere cap complex;nuclear chromosome, telomeric region;fibrillar center;nucleus;nucleoplasm;nucleolus;cytoplasm;spindle;nuclear body;shelterin complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;double-stranded telomeric DNA binding;telomerase activity;protein binding;DNA binding, bending;telomeric DNA binding;protein homodimerization activity;ankyrin repeat binding;G-rich strand telomeric DNA binding