TIMP2
TIMP metallopeptidase inhibitor 2, the group of Tissue inhibitor of metallopeptidases
Basic information
Region (hg38): 17:78852977-78925387
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 TIMP2 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 | 4 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 10 | 3 | 2 |
Variants in TIMP2
This is a list of pathogenic ClinVar variants found in the TIMP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-78855707-G-A | not specified | Uncertain significance (Oct 06, 2021) | ||
| 17-78855712-G-A | TIMP2-related disorder | Likely benign (May 09, 2022) | ||
| 17-78855717-G-A | not specified | Uncertain significance (Apr 20, 2024) | ||
| 17-78855756-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 17-78855812-A-G | not specified | Uncertain significance (Apr 08, 2022) | ||
| 17-78857541-T-A | not specified | Uncertain significance (May 24, 2023) | ||
| 17-78857596-C-T | not specified | Uncertain significance (Jan 31, 2023) | ||
| 17-78857625-T-C | not specified | Uncertain significance (Dec 20, 2023) | ||
| 17-78857629-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 17-78857638-C-T | not specified | Uncertain significance (Jun 03, 2022) | ||
| 17-78870935-C-T | TIMP2-related disorder | Benign (Jun 11, 2019) | ||
| 17-78873811-A-G | TIMP2-related disorder | Benign (Feb 18, 2019) | ||
| 17-78873857-G-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 17-78873903-C-T | TIMP2-related disorder | Likely benign (Sep 06, 2019) | ||
| 17-78892237-G-A | Likely benign (Jun 01, 2024) | |||
| 17-78925022-G-A | not specified | Uncertain significance (Feb 01, 2023) | ||
| 17-78925053-G-A | TIMP2-related disorder | Benign (Oct 21, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TIMP2 | protein_coding | protein_coding | ENST00000262768 | 5 | 72411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.789 | 0.210 | 125545 | 0 | 2 | 125547 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.61 | 71 | 121 | 0.589 | 0.00000747 | 1444 |
| Missense in Polyphen | 20 | 51.63 | 0.38737 | 594 | ||
| Synonymous | -0.0323 | 54 | 53.7 | 1.01 | 0.00000436 | 408 |
| Loss of Function | 2.56 | 1 | 9.50 | 0.105 | 4.04e-7 | 123 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Complexes with metalloproteinases (such as collagenases) and irreversibly inactivates them by binding to their catalytic zinc cofactor. Known to act on MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-13, MMP-14, MMP-15, MMP-16 and MMP-19. {ECO:0000269|PubMed:11710594, ECO:0000269|PubMed:2554304, ECO:0000269|PubMed:2793861}.;
- Pathway
- Matrix Metalloproteinases;Angiogenesis;Angiogenesis overview;IL1 and megakaryocytes in obesity;Vitamin D Receptor Pathway;Protein alkylation leading to liver fibrosis;Neutrophil degranulation;inhibition of matrix metalloproteinases;Extracellular matrix organization;Innate Immune System;Immune System;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix
(Consensus)
Intolerance Scores
- loftool
- 0.197
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.299
- hipred
- N
- hipred_score
- 0.472
- ghis
- 0.657
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.760
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Timp2
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- timp2a
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- central nervous system development;aging;negative regulation of cell population proliferation;response to hormone;response to organic substance;negative regulation of endopeptidase activity;extracellular matrix disassembly;regulation of Rap protein signal transduction;response to cytokine;response to drug;neutrophil degranulation;positive regulation of MAPK cascade;positive regulation of neuron differentiation;positive regulation of adenylate cyclase activity;negative regulation of mitotic cell cycle;negative regulation of Ras protein signal transduction;negative regulation of membrane protein ectodomain proteolysis;negative regulation of metallopeptidase activity
- Cellular component
- extracellular region;extracellular space;cell surface;growth cone;extracellular matrix;specific granule lumen;neuronal cell body;collagen-containing extracellular matrix;tertiary granule lumen;ficolin-1-rich granule lumen
- Molecular function
- protease binding;integrin binding;protein binding;metalloendopeptidase inhibitor activity;zinc ion binding;peptidase inhibitor activity