DUSP16

dual specificity phosphatase 16, the group of MAP kinase phosphatases

Basic information

Region (hg38): 12:12473281-12562863

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.

• Inborn genetic diseases (23 variants)
• not provided (6 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.

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				4		4
missense			23			23
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	4	1

Variants in DUSP16

This is a list of pathogenic ClinVar variants found in the DUSP16 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12476864-G-A		not specified	Uncertain significance (Apr 28, 2022)
12-12476933-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-12476958-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-12477039-G-A		not specified	Uncertain significance (Jan 18, 2023)
12-12477051-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-12477116-A-G		not specified	Uncertain significance (May 04, 2022)
12-12477131-T-C		not specified	Uncertain significance (Jun 12, 2023)
12-12477188-G-A		not specified	Uncertain significance (Mar 11, 2024)
12-12477245-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-12477279-G-A		not specified	Uncertain significance (Jul 13, 2021)
12-12477374-G-A		not specified	Uncertain significance (Aug 17, 2021)
12-12477476-G-C		not specified	Uncertain significance (Nov 27, 2023)
12-12477519-C-T		not specified	Uncertain significance (Nov 15, 2021)
12-12477673-G-A			Likely benign (Feb 01, 2023)
12-12477707-G-A		not specified	Uncertain significance (Dec 22, 2023)
12-12477747-TGGGC-T			Benign (Dec 31, 2019)
12-12477751-C-T			Likely benign (Apr 01, 2022)
12-12477756-T-C		not specified	Uncertain significance (Jan 29, 2024)
12-12477759-C-T		not specified	Uncertain significance (Dec 26, 2023)
12-12477789-C-T		not specified	Uncertain significance (Nov 18, 2022)
12-12477843-C-T		not specified	Uncertain significance (Mar 07, 2024)
12-12477851-G-A		not specified	Uncertain significance (Dec 12, 2023)
12-12477906-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-12477915-C-G		not specified	Uncertain significance (Nov 09, 2021)
12-12477923-C-T		not specified	Uncertain significance (Sep 06, 2022)

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