DUSP9

dual specificity phosphatase 9, the group of MAP kinase phosphatases

Basic information

Region (hg38): X:153642491-153651326

Links

ENSG00000130829 ∙ NCBI:1852 ∙ OMIM:300134 ∙ HGNC:3076 ∙ Uniprot:Q99956 ∙ 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 DUSP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP9 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	4
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	3

Variants in DUSP9

This is a list of pathogenic ClinVar variants found in the DUSP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153648006-C-A		not specified	Uncertain significance (May 14, 2024)
X-153648006-C-T		not specified	Uncertain significance (Oct 02, 2023)
X-153648119-A-G		not specified	Uncertain significance (Apr 04, 2024)
X-153648209-G-T		not specified	Uncertain significance (Mar 02, 2023)
X-153648221-C-T		not specified	Uncertain significance (Nov 22, 2023)
X-153648240-A-C		not specified	Uncertain significance (Feb 09, 2022)
X-153648313-C-A			Likely benign (Jul 01, 2022)
X-153649266-C-G		not specified	Uncertain significance (Oct 17, 2023)
X-153649292-G-A		not specified	Uncertain significance (Mar 13, 2023)
X-153649297-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-153649310-C-T			Benign (Apr 13, 2018)
X-153649313-C-T			Uncertain significance (Feb 15, 2019)
X-153649332-C-T			Benign (Jun 14, 2018)
X-153649333-G-C		not specified	Uncertain significance (Dec 12, 2023)
X-153649380-G-A			Benign (Apr 13, 2018)
X-153649387-G-A		not specified	Uncertain significance (Feb 17, 2023)
X-153649399-G-A		not specified	Uncertain significance (Oct 04, 2022)
X-153649424-C-T		not specified	Uncertain significance (Dec 30, 2023)
X-153649456-C-T		not specified	Uncertain significance (Jun 16, 2024)
X-153649457-G-A		not specified	Uncertain significance (Jun 11, 2024)
X-153649537-A-G		not specified	Uncertain significance (Jun 07, 2024)
X-153649564-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-153650002-C-G		not specified	Uncertain significance (Jul 05, 2023)
X-153650174-C-T		not specified	Uncertain significance (Feb 15, 2023)
X-153650175-G-A		not specified	Uncertain significance (Apr 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP9	protein_coding	protein_coding	ENST00000342782	3	8836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.820	0.176	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	99	144	0.689	0.0000124	2417
Missense in Polyphen		26	61.357	0.42375		1231
Synonymous	0.0168	69	69.2	0.997	0.00000624	859
Loss of Function	2.20	0	5.66	0.00	3.80e-7	117

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inactivates MAP kinases. Has a specificity for the ERK family.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;MAPK Signaling Pathway;Signal Transduction;regulation of map kinase pathways through dual specificity phosphatases;RAF-independent MAPK1/3 activation;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.144

Haploinsufficiency Scores

• pHI: 0.585
• hipred: Y
• hipred_score: 0.813
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.611

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp9
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

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