DUSP16

dual specificity phosphatase 16, the group of MAP kinase phosphatases

Basic information

Region (hg38): 12:12473282-12562863

Links

ENSG00000111266

∙ NCBI:80824 ∙ OMIM:607175 ∙ HGNC:17909 ∙ Uniprot:Q9BY84 ∙ 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 DUSP16 gene.

not_specified (65 variants)
not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030640.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			65 clinvar			65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	4	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP16	protein_coding	protein_coding	ENST00000228862	6	86489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0889	0.911	115488	1106	9154	125748	0.0417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.890	329	378	0.871	0.0000211	4345
Missense in Polyphen		67	111.6	0.60036		1243
Synonymous	-0.191	159	156	1.02	0.00000922	1336
Loss of Function	3.48	7	26.2	0.267	0.00000143	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.231	0.227
Ashkenazi Jewish	0.0198	0.00947
East Asian	0.438	0.173
Finnish	0.0429	0.0209
European (Non-Finnish)	0.00854	0.00417
Middle Eastern	0.438	0.173
South Asian	0.216	0.0945
Other	0.0605	0.0279

dbNSFP

Source: dbNSFP

Function: FUNCTION: Dual specificity protein phosphatase involved in the inactivation of MAP kinases. Dephosphorylates MAPK10 bound to ARRB2. {ECO:0000269|PubMed:11489891, ECO:0000269|PubMed:15888437}.;
Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;MAPK Signaling Pathway;Signal Transduction;RAF-independent MAPK1/3 activation;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Regulation of p38-alpha and p38-beta (Consensus)

Recessive Scores

pRec: 0.121

Intolerance Scores

loftool: 0.551
rvis_EVS: -0.78
rvis_percentile_EVS: 13.05

Haploinsufficiency Scores

pHI: 0.816
hipred: Y
hipred_score: 0.704
ghis: 0.591

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dusp16
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); hematopoietic system phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: inactivation of MAPK activity;protein dephosphorylation;dephosphorylation;peptidyl-tyrosine dephosphorylation;MAPK export from nucleus;MAPK phosphatase export from nucleus, leptomycin B sensitive
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;cytoplasmic vesicle
Molecular function: phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity;phosphatase activity;MAP kinase tyrosine/serine/threonine phosphatase activity