DUSP3
dual specificity phosphatase 3, the group of Atypical dual specificity phosphatases
Basic information
Region (hg38): 17:43766125-43778977
Previous symbols: [ "VHR" ]
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 DUSP3 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 | 1 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 1 | 0 |
Variants in DUSP3
This is a list of pathogenic ClinVar variants found in the DUSP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-43769803-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 17-43769811-C-T | not specified | Uncertain significance (Aug 22, 2023) | ||
| 17-43774739-T-C | not specified | Uncertain significance (Dec 13, 2023) | ||
| 17-43774820-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 17-43774843-T-C | not specified | Uncertain significance (Apr 27, 2022) | ||
| 17-43774881-G-A | Likely benign (Jul 01, 2022) | |||
| 17-43778870-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
| 17-43778897-G-C | not specified | Uncertain significance (Apr 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DUSP3 | protein_coding | protein_coding | ENST00000226004 | 3 | 12868 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.462 | 0.515 | 125742 | 0 | 4 | 125746 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 78 | 112 | 0.699 | 0.00000690 | 1211 |
| Missense in Polyphen | 38 | 51.84 | 0.73302 | 486 | ||
| Synonymous | 0.676 | 42 | 48.0 | 0.876 | 0.00000320 | 360 |
| Loss of Function | 1.82 | 1 | 5.67 | 0.176 | 2.47e-7 | 69 |
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) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Shows activity both for tyrosine-protein phosphate and serine-protein phosphate, but displays a strong preference toward phosphotyrosines. Specifically dephosphorylates and inactivates ERK1 and ERK2. {ECO:0000269|PubMed:10224087, ECO:0000269|PubMed:11863439}.;
- Pathway
- MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;MAPK Signaling Pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;TCR;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);ERKs are inactivated;Signaling by NTRK1 (TRKA);Signaling by NTRKs;ERK/MAPK targets;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade
(Consensus)
Recessive Scores
- pRec
- 0.212
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.329
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dusp3
- Phenotype
- homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype;
Gene ontology
- Biological process
- inactivation of MAPK activity;dephosphorylation;negative regulation of cell migration;peptidyl-tyrosine dephosphorylation;negative regulation of epidermal growth factor receptor signaling pathway;negative regulation of MAPK cascade;positive regulation of mitotic cell cycle;negative regulation of JNK cascade;negative regulation of T cell receptor signaling pathway;negative regulation of T cell activation;negative regulation of chemotaxis;regulation of focal adhesion assembly;negative regulation of ERK1 and ERK2 cascade;cellular response to epidermal growth factor stimulus;positive regulation of focal adhesion disassembly;peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity
- Cellular component
- immunological synapse;nucleus;nucleoplasm;cytosol
- Molecular function
- protein tyrosine phosphatase activity;cytoskeletal protein binding;protein tyrosine/serine/threonine phosphatase activity;phosphatase activity;protein kinase binding;receptor tyrosine kinase binding;MAP kinase phosphatase activity;protein tyrosine kinase binding