TIPRL
Basic information
Region (hg38): 1:168178962-168202109
Links
Phenotypes
GenCC
Source:
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 TIPRL 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in TIPRL
This is a list of pathogenic ClinVar variants found in the TIPRL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-168179168-G-A | not specified | Uncertain significance (May 12, 2024) | ||
| 1-168183909-G-A | not specified | Uncertain significance (Feb 02, 2022) | ||
| 1-168184041-A-G | not specified | Uncertain significance (Jun 16, 2023) | ||
| 1-168191381-A-G | not specified | Uncertain significance (Mar 14, 2024) | ||
| 1-168191428-G-T | not specified | Uncertain significance (May 16, 2024) | ||
| 1-168191489-A-C | not specified | Uncertain significance (Apr 08, 2022) | ||
| 1-168196550-G-A | not specified | Uncertain significance (May 11, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TIPRL | protein_coding | protein_coding | ENST00000367833 | 7 | 21780 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.954 | 0.0463 | 125729 | 0 | 2 | 125731 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.80 | 84 | 145 | 0.580 | 0.00000701 | 1809 |
| Missense in Polyphen | 16 | 51.847 | 0.3086 | 658 | ||
| Synonymous | 0.697 | 47 | 53.5 | 0.879 | 0.00000294 | 477 |
| Loss of Function | 3.23 | 1 | 14.1 | 0.0712 | 7.70e-7 | 183 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be a allosteric regulator of serine/threonine- protein phosphatase 2A (PP2A). Isoform 1 inhibits catalytic activity of the PP2A(D) core complex in vitro. The PP2A(C):TIPRL complex does not show phosphatase activity. Acts as negative regulator of serine/threonine-protein phosphatase 4 probably by inhibiting the formation of the active PPP4C:PPP4R2 complex; the function is proposed to implicate it in DNA damage response by promoting H2AFX phosphorylated on Ser-140 (gamma-H2AFX). May play a role in the regulation of ATM/ATR signaling pathway controlling DNA replication and repair. {ECO:0000269|PubMed:17384681, ECO:0000269|PubMed:26717153}.;
Recessive Scores
- pRec
- 0.0849
Intolerance Scores
- loftool
- 0.230
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.28
Haploinsufficiency Scores
- pHI
- 0.169
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.585
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tiprl
- Phenotype
Zebrafish Information Network
- Gene name
- tiprl
- Affected structure
- apoptotic chromosome condensation
- Phenotype tag
- abnormal
- Phenotype quality
- increased occurrence
Gene ontology
- Biological process
- DNA damage checkpoint;signal transduction;TOR signaling;negative regulation of phosphoprotein phosphatase activity
- Cellular component
- cytosol
- Molecular function
- protein binding