DUSP4

dual specificity phosphatase 4, the group of MAP kinase phosphatases

Basic information

Region (hg38): 8:29333064-29350684

Links

ENSG00000120875 ∙ NCBI:1846 ∙ OMIM:602747 ∙ HGNC:3070 ∙ Uniprot:Q13115 ∙ 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 DUSP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP4 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				2		2
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in DUSP4

This is a list of pathogenic ClinVar variants found in the DUSP4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-29337037-G-C		not specified	Uncertain significance (Jul 12, 2022)
8-29337061-G-C		not specified	Uncertain significance (Jun 05, 2023)
8-29337091-C-T		not specified	Uncertain significance (Aug 02, 2021)
8-29337097-C-T		not specified	Uncertain significance (May 13, 2024)
8-29337118-C-T		not specified	Uncertain significance (May 01, 2024)
8-29337139-C-G		not specified	Likely benign (Dec 20, 2023)
8-29337189-G-A		not specified	Likely benign (Sep 09, 2024)
8-29337190-C-A		not specified	Uncertain significance (Oct 10, 2023)
8-29337273-C-T		not specified	Uncertain significance (Apr 25, 2022)
8-29337283-C-T		not specified	Uncertain significance (Sep 30, 2024)
8-29337365-C-T			Likely benign (Mar 01, 2023)
8-29337391-C-T		not specified	Uncertain significance (Apr 23, 2024)
8-29338344-G-C		not specified	Uncertain significance (Jan 19, 2024)
8-29338413-G-T		not specified	Uncertain significance (Mar 20, 2024)
8-29338443-C-T		not specified	Uncertain significance (Oct 05, 2023)
8-29338444-G-A		not specified	Uncertain significance (Sep 06, 2022)
8-29338484-G-C		not specified	Uncertain significance (Oct 05, 2023)
8-29338487-C-A		not specified	Uncertain significance (Mar 16, 2022)
8-29340104-G-A			Likely benign (Nov 01, 2022)
8-29340112-G-C		not specified	Uncertain significance (Aug 12, 2024)
8-29340139-C-A		not specified	Uncertain significance (Nov 10, 2022)
8-29340145-G-C		not specified	Uncertain significance (Sep 21, 2023)
8-29340168-G-A		not specified	Uncertain significance (May 25, 2022)
8-29340169-G-A		not specified	Uncertain significance (May 15, 2024)
8-29340181-C-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP4	protein_coding	protein_coding	ENST00000240100	4	17605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.882	0.118	125522	0	5	125527	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	179	245	0.732	0.0000142	2519
Missense in Polyphen		49	92.634	0.52896		923
Synonymous	0.615	104	112	0.926	0.00000714	836
Loss of Function	2.84	1	11.3	0.0882	4.82e-7	141

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)	0.0000493	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates mitogenic signal transduction by dephosphorylating both Thr and Tyr residues on MAP kinases ERK1 and ERK2. {ECO:0000269|PubMed:7535768}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;Endoderm Differentiation;MAPK Signaling Pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;regulation of map kinase pathways through dual specificity phosphatases;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;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);RAF-independent MAPK1/3 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;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;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: 0.312

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.831
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dusp4
• Phenotype: hematopoietic system phenotype; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: dusp4
• Affected structure: endodermal cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: inactivation of MAPK activity;dephosphorylation;peptidyl-tyrosine dephosphorylation;peptidyl-threonine dephosphorylation;negative regulation of ERK1 and ERK2 cascade
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;protein tyrosine/threonine phosphatase activity;phosphatase activity;MAP kinase tyrosine/serine/threonine phosphatase activity;MAP kinase serine/threonine phosphatase activity