DUSP28

dual specificity phosphatase 28, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 2:240560054-240565256

Links

ENSG00000188542 ∙ NCBI:285193 ∙ ∙ HGNC:33237 ∙ Uniprot:Q4G0W2 ∙ 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 DUSP28 gene.

• not_specified (54 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP28 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001370465.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			53	1		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP28	protein_coding	protein_coding	ENST00000405954	2	3961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.180	0.657	125456	0	1	125457	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	105	78.7	1.33	0.00000365	1046
Missense in Polyphen		39	28.303	1.378		411
Synonymous	-0.913	43	36.0	1.19	0.00000182	389
Loss of Function	0.878	1	2.50	0.400	1.06e-7	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has phosphatase activity with the synthetic substrate 6,8-difluoro-4-methylumbelliferyl phosphate (in vitro) (PubMed:24531476, PubMed:29121083). Has almost no detectable activity with phosphotyrosine, even less activity with phosphothreonine and displays complete lack of activity with phosphoserine (PubMed:29121083). The poor activity with phosphotyrosine may be due to steric hindrance by bulky amino acid sidechains that obstruct access to the active site (PubMed:29121083). {ECO:0000269|PubMed:24531476, ECO:0000269|PubMed:29121083}.

Recessive Scores

• pRec: 0.128

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.292
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp28

Gene ontology

• Biological process: dephosphorylation;peptidyl-tyrosine dephosphorylation
• Molecular function: protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity;phosphatase activity