DUSP5

dual specificity phosphatase 5, the group of MAP kinase phosphatases

Basic information

Region (hg38): 10:110497907-110511533

Links

ENSG00000138166 ∙ NCBI:1847 ∙ OMIM:603069 ∙ HGNC:3071 ∙ Uniprot:Q16690 ∙ 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 DUSP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP5 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	2
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in DUSP5

This is a list of pathogenic ClinVar variants found in the DUSP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-110498205-C-G		not specified	Uncertain significance (Nov 24, 2024)
10-110498209-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-110498233-A-T		not specified	Uncertain significance (Jul 17, 2023)
10-110498239-C-T		not specified	Uncertain significance (Aug 14, 2024)
10-110498260-C-T		not specified	Uncertain significance (Mar 29, 2023)
10-110498261-T-C		not specified	Uncertain significance (Feb 27, 2024)
10-110498284-G-T			Benign (Feb 16, 2018)
10-110498288-G-C		not specified	Uncertain significance (Dec 06, 2023)
10-110498303-C-G		not specified	Uncertain significance (Nov 15, 2021)
10-110498312-A-G		not specified	Uncertain significance (May 13, 2024)
10-110498325-C-A		not specified	Uncertain significance (Dec 22, 2023)
10-110498354-A-T		not specified	Uncertain significance (Aug 17, 2021)
10-110498401-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-110502729-G-C		not specified	Uncertain significance (Feb 05, 2024)
10-110502761-C-T			Likely benign (Apr 01, 2022)
10-110502762-G-T		not specified	Uncertain significance (Nov 26, 2024)
10-110502765-G-A		not specified	Uncertain significance (Aug 21, 2024)
10-110502768-G-A		not specified	Uncertain significance (Mar 23, 2023)
10-110502820-A-G		not specified	Uncertain significance (Sep 09, 2024)
10-110502832-C-G		not specified	Uncertain significance (May 28, 2024)
10-110506997-C-G		not specified	Uncertain significance (Mar 20, 2023)
10-110510088-A-C		not specified	Uncertain significance (Dec 13, 2022)
10-110510125-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-110510140-T-C		not specified	Uncertain significance (Jun 26, 2024)
10-110510142-G-A		not specified	Uncertain significance (Nov 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP5	protein_coding	protein_coding	ENST00000369583	4	13707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00332	0.954	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.694	182	210	0.865	0.0000108	2410
Missense in Polyphen		35	56.807	0.61612		677
Synonymous	-0.559	102	95.1	1.07	0.00000535	811
Loss of Function	1.77	6	12.9	0.466	5.46e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000528	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual specificity protein phosphatase; active with phosphotyrosine, phosphoserine and phosphothreonine residues. The highest relative activity is toward ERK1. {ECO:0000269|PubMed:7961985}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;Endoderm Differentiation;Signal Transduction;ATF-2 transcription factor network;RAF-independent MAPK1/3 activation;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.252

Intolerance Scores

• loftool: 0.375
• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.52

Haploinsufficiency Scores

• pHI: 0.383
• hipred: Y
• hipred_score: 0.800
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp5
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; neoplasm; immune system phenotype; hematopoietic system phenotype

Gene ontology

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