DUSP12

dual specificity phosphatase 12, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 1:161749757-161757238

Links

ENSG00000081721 ∙ NCBI:11266 ∙ OMIM:604835 ∙ HGNC:3067 ∙ Uniprot:Q9UNI6 ∙ 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 DUSP12 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP12 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						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in DUSP12

This is a list of pathogenic ClinVar variants found in the DUSP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161749826-G-A		not specified	Uncertain significance (Oct 21, 2021)
1-161749866-G-C		not specified	Likely benign (Dec 11, 2023)
1-161749875-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-161749985-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-161749988-G-A		not specified	Uncertain significance (Nov 21, 2022)
1-161750031-G-A		not specified	Uncertain significance (Dec 16, 2022)
1-161750060-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-161750103-T-C		not specified	Uncertain significance (Nov 19, 2022)
1-161751718-A-C		not specified	Uncertain significance (Dec 09, 2023)
1-161751907-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-161751959-A-C		not specified	Uncertain significance (Sep 12, 2023)
1-161751966-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-161751981-C-G		not specified	Uncertain significance (Oct 27, 2023)
1-161753113-G-A		not specified	Likely benign (Dec 21, 2023)
1-161753143-A-C		not specified	Uncertain significance (Sep 27, 2021)
1-161753146-A-G		not specified	Uncertain significance (Mar 01, 2024)
1-161753226-A-G		not specified	Uncertain significance (May 18, 2023)
1-161756789-C-A		not specified	Uncertain significance (Feb 28, 2023)
1-161756789-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-161756841-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-161756864-A-G		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP12	protein_coding	protein_coding	ENST00000367943	6	7481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000139	0.965	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.580	169	192	0.882	0.00000894	2217
Missense in Polyphen		57	66.737	0.8541		821
Synonymous	0.604	63	69.4	0.908	0.00000310	652
Loss of Function	1.90	9	17.6	0.512	9.45e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000661	0.000661
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual specificity phosphatase; can dephosphorylate both phosphotyrosine and phosphoserine or phosphothreonine residues. Can dephosphorylate glucokinase (in vitro) (By similarity). Has phosphatase activity with the synthetic substrate 6,8-difluoro-4- methylumbelliferyl phosphate and other in vitro substrates (PubMed:10446167, PubMed:24531476). {ECO:0000250|UniProtKB:Q9JIM4, ECO:0000269|PubMed:10446167, ECO:0000269|PubMed:24531476}.

Recessive Scores

• pRec: 0.172

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.331
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp12

Gene ontology

• Biological process: cellular protein modification process;protein dephosphorylation;dephosphorylation;positive regulation of glucokinase activity;peptidyl-tyrosine dephosphorylation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: nucleic acid binding;protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;zinc ion binding;phosphatase activity;kinase binding