DUSP3

dual specificity phosphatase 3, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 17:43766124-43778977

Previous symbols: [ "VHR" ]

Links

ENSG00000108861 ∙ NCBI:1845 ∙ OMIM:600183 ∙ HGNC:3069 ∙ Uniprot:P51452 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DUSP3 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

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		1
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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