TERF1
telomeric repeat binding factor 1, the group of Shelterin complex|Myb/SANT domain containing
Basic information
Region (hg38): 8:73008856-73048123
Previous symbols: [ "TRBF1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 6 | |||||
| missense | 15 | 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:
| 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:
- 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