DUSP13B

dual specificity phosphatase 13B, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 10:75094432-75109206

Previous symbols: [ "DUSP13" ]

Links

ENSG00000293542 ∙ NCBI:51207 ∙ OMIM:613191 ∙ HGNC:19681 ∙ Uniprot:Q6B8I1, Q9UII6 ∙ 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 DUSP13B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP13B 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				1		1
missense			23	1	3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	23	2	5

Variants in DUSP13B

This is a list of pathogenic ClinVar variants found in the DUSP13B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-75094683-C-T		not specified	Uncertain significance (Jun 25, 2024)
10-75094684-G-A		not specified	Uncertain significance (Nov 25, 2024)
10-75094689-G-A		not specified	Uncertain significance (Aug 08, 2023)
10-75094696-G-A		not specified	Uncertain significance (Jun 10, 2022)
10-75094704-C-T			Benign (May 15, 2018)
10-75094705-G-C			Benign (May 15, 2018)
10-75094723-G-C		not specified	Uncertain significance (Jan 10, 2022)
10-75094728-C-T		not specified	Uncertain significance (May 17, 2023)
10-75094729-G-A		not specified	Uncertain significance (Feb 17, 2022)
10-75094749-C-A		not specified	Uncertain significance (Feb 21, 2024)
10-75094758-C-T		not specified	Uncertain significance (Aug 12, 2021)
10-75094773-G-A		not specified	Uncertain significance (Sep 30, 2024)
10-75094806-C-T			Benign (Feb 17, 2020)
10-75094821-G-T		not specified	Uncertain significance (Apr 26, 2023)
10-75094842-C-T		not specified	Uncertain significance (Mar 15, 2024)
10-75094843-G-A		not specified	Uncertain significance (May 17, 2023)
10-75094855-T-A		not specified	Uncertain significance (Jul 27, 2022)
10-75094875-C-T		not specified	Uncertain significance (Oct 20, 2021)
10-75094876-G-A		not specified	Uncertain significance (Mar 29, 2023)
10-75095584-C-T		not specified	Likely benign (Aug 03, 2022)
10-75095592-G-C		not specified	Uncertain significance (Jun 17, 2024)
10-75095607-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-75095610-G-T		not specified	Uncertain significance (Mar 21, 2023)
10-75095692-G-A		not specified	Uncertain significance (Jul 25, 2024)
10-75095723-C-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP13B	protein_coding	protein_coding	ENST00000372700	4	14788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000113	0.602	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.322	149	160	0.928	0.0000107	1586
Missense in Polyphen		50	56.907	0.87863		578
Synonymous	-0.421	69	64.7	1.07	0.00000400	536
Loss of Function	0.835	9	12.1	0.741	8.45e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000478	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.000168	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable protein tyrosine phosphatase. Has phosphatase activity with synthetic substrates (PubMed:15252030, PubMed:29106959). Has a phosphatase activity-independent regulatory role in MAP3K5/ASK1-mediated apoptosis, preventing MAP3K5/ASK1 inhibition by AKT1. Shows no phosphatase activity on MAPK1/ERK2, MAPK8/JNK, MAPK14/p38 and MAP3K5/ASK1. {ECO:0000269|PubMed:15252030, ECO:0000269|PubMed:20358250, ECO:0000269|PubMed:29106959}.

Recessive Scores

• pRec: 0.0920

Intolerance Scores

• loftool: 0.319
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.97

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.144
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.657

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp13

Gene ontology

• Biological process: protein dephosphorylation;spermatogenesis;dephosphorylation;peptidyl-tyrosine dephosphorylation;meiotic cell cycle
• Molecular function: protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;phosphatase activity