TERF2IP
TERF2 interacting protein, the group of Shelterin complex
Basic information
Region (hg38): 16:75647773-75761872
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (764 variants)
- not_provided (133 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TERF2IP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018975.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 281 | 281 | ||||
| missense | 497 | 13 | 510 | |||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 0 | 1 | 500 | 294 | 0 |
Highest pathogenic variant AF is 0.0000050167846
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TERF2IP | protein_coding | protein_coding | ENST00000300086 | 3 | 114087 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000267 | 0.781 | 125725 | 0 | 23 | 125748 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0292 | 225 | 224 | 1.01 | 0.0000106 | 2565 |
| Missense in Polyphen | 44 | 51.579 | 0.85305 | 599 | ||
| Synonymous | -1.18 | 107 | 92.6 | 1.16 | 0.00000453 | 794 |
| Loss of Function | 1.18 | 9 | 13.7 | 0.655 | 6.73e-7 | 166 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000399 | 0.000398 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000110 | 0.000105 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'- TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes. {ECO:0000269|PubMed:16166375, ECO:0000269|PubMed:19763083}.;
- Pathway
- Splicing factor NOVA regulated synaptic proteins;Packaging Of Telomere Ends;Telomere Maintenance;Chromosome Maintenance;Cell Cycle;Regulation of Telomerase
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.462
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.550
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Terf2ip
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; pigmentation 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); liver/biliary system phenotype; immune system phenotype;
Gene ontology
- Biological process
- telomere maintenance;negative regulation of protein phosphorylation;regulation of transcription, DNA-templated;telomere maintenance via telomerase;regulation of double-strand break repair via homologous recombination;telomere maintenance via telomere lengthening;telomere capping;protection from non-homologous end joining at telomere;regulation of telomere maintenance;negative regulation of telomere maintenance;positive regulation of peptidyl-serine phosphorylation;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of DNA recombination at telomere;positive regulation of NF-kappaB transcription factor activity;protein localization to chromosome, telomeric region;positive regulation of NIK/NF-kappaB signaling;positive regulation of protein acetylation
- Cellular component
- nuclear chromosome;chromosome, telomeric region;nuclear telomere cap complex;nuclear chromosome, telomeric region;nucleus;nuclear envelope;nucleoplasm;cytoplasm;cytosol;nuclear body;Mre11 complex;shelterin complex
- Molecular function
- protein binding;phosphatase binding;telomeric DNA binding;G-rich strand telomeric DNA binding