DUSP13A

Summary

DUSP13A (dual specificity phosphatase 13A, HGNC:56772) is a protein-coding gene on chromosome 10q22.2, encoding Dual specificity protein phosphatase 13A (Q6B8I1). Probable protein tyrosine phosphatase.

Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in skeletal muscle.

Source: NCBI Gene 128854680 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic
• MANE Select transcript: NM_001007271

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56772
Approved symbol	DUSP13A
Name	dual specificity phosphatase 13A
Location	10q22.2
Locus type	gene with protein product
Status	Approved
Aliases	MDSP, BEDP
Ensembl gene	ENSG00000293543
Ensembl biotype	protein_coding
Entrez	128854680

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 nonsense_mediated_decay, 3 protein_coding

ENST00000308475, ENST00000372702, ENST00000479884, ENST00000494588, ENST00000707122, ENST00000713560

RefSeq mRNA: 1 — MANE Select: NM_001007271 NM_001007271

CCDS: CCDS53542

Canonical transcript exons

ENST00000713560 — 3 exons

Exon	Start	End
ENSE00003625302	75107992	75108209
ENSE00004020305	75109009	75109157
ENSE00004020306	75105669	75105868

Expression profiles

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting DUSP13A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-4293	99.22	65.46	1263
HSA-MIR-6744-3P	99.22	64.41	972
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-4757-5P	99.12	64.51	981
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-1288-5P	98.85	67.01	734
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-198	98.70	67.32	920
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-4436B-3P	98.25	65.26	1494
HSA-MIR-6735-5P	98.24	65.36	1488
HSA-MIR-7843-5P	98.12	65.26	1421

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-223p8.8	ENSDARG00000092650
mus_musculus	Dusp13a	ENSMUSG00000121906

Paralogs (31): DUSP13B (ENSG00000079393), DUSP12 (ENSG00000081721), SSH1 (ENSG00000084112), DUSP3 (ENSG00000108861), PTPMT1 (ENSG00000110536), DUSP16 (ENSG00000111266), EPM2A (ENSG00000112425), DUSP22 (ENSG00000112679), DUSP1 (ENSG00000120129), DUSP4 (ENSG00000120875), STYXL1 (ENSG00000127952), DUSP9 (ENSG00000130829), DUSP26 (ENSG00000133878), DUSP5 (ENSG00000138166), DUSP6 (ENSG00000139318), SSH2 (ENSG00000141298), DUSP10 (ENSG00000143507), DUSP15 (ENSG00000149599), DUSP2 (ENSG00000158050), KASH5 (ENSG00000161609), DUSP19 (ENSG00000162999), DUSP7 (ENSG00000164086), DUSP18 (ENSG00000167065), SSH3 (ENSG00000172830), DUSP8 (ENSG00000184545), DUSP28 (ENSG00000188542), DUSP29 (ENSG00000188716), DUSP21 (ENSG00000189037), STYX (ENSG00000198252), STYXL2 (ENSG00000198842), DUSP14 (ENSG00000276023)

Protein

Protein identifiers

Dual specificity protein phosphatase 13A — Q6B8I1 (reviewed: Q6B8I1)

Alternative names: Branching-enzyme interacting DSP, Muscle-restricted DSP

All UniProt accessions (2): A0A9L9PYL3, Q6B8I1

UniProt curated annotations — full annotation on UniProt →

Function. Probable protein tyrosine phosphatase. Has phosphatase activity with synthetic substrates. 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.

Subunit / interactions. Monomer. Interacts with MAP3K5/ASK1; may compete with AKT1 preventing MAP3K5/ASK1 phosphorylation by AKT1.

Subcellular location. Cytoplasm.

Tissue specificity. Skeletal muscle specific.

Activity regulation. Inhibited by vanadate.

Miscellaneous. Produced by alternative promoter usage. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily.

Isoforms (5)

UniProt ID	Names	Canonical?
Q6B8I1-1	5	yes
Q6B8I1-5	2
Q6B8I1-2	6
Q6B8I1-3	7
Q6B8I1-4	8

RefSeq proteins (1): NP_001007272* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000340	Dual-sp_phosphatase_cat-dom	Domain
IPR000387	Tyr_Pase_dom	Domain
IPR003595	Tyr_Pase_cat	Domain
IPR016130	Tyr_Pase_AS	Active_site
IPR020405	Atypical_DUSP_subfamA	Family
IPR020422	TYR_PHOSPHATASE_DUAL_dom	Domain
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily

Pfam: PF00782

Catalyzed reactions (Rhea), 3 shown:

• O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)
• O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate (RHEA:20629)
• O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate (RHEA:47004)

UniProt features (31 total): strand 9, helix 8, splice variant 6, mutagenesis site 2, sequence conflict 2, chain 1, domain 1, active site 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
5XJV	X-RAY DIFFRACTION	1.69

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6B8I1-F1	90.30	0.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 129 (phosphocysteine intermediate)

Mutagenesis-validated functional residues (2):

Position	Phenotype
97	no effect on interaction with map3k5.
129	loss of enzyme activity. no effect on interaction with map3k5.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): GOBP_DEPHOSPHORYLATION, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_PROTEIN_SERINE_THREONINE_PHOSPHATASE_ACTIVITY, GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY, GOMF_PROTEIN_TYROSINE_SERINE_THREONINE_PHOSPHATASE_ACTIVITY, GOMF_PROTEIN_TYROSINE_PHOSPHATASE_ACTIVITY, GOMF_PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY, GOMF_PHOSPHATASE_ACTIVITY, MIR3680_3P, MIR1207_5P, MIR146A_3P, MIR4640_5P, MIR4436B_3P, MIR6879_5P, MIR6735_5P

GO Biological Process (2): dephosphorylation (GO:0016311), protein dephosphorylation (GO:0006470)

GO Molecular Function (6): protein serine/threonine phosphatase activity (GO:0004722), protein tyrosine phosphatase activity (GO:0004725), protein tyrosine/serine/threonine phosphatase activity (GO:0008138), phosphatase activity (GO:0016791), phosphoprotein phosphatase activity (GO:0004721), hydrolase activity (GO:0016787)

GO Cellular Component (2): cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphoprotein phosphatase activity	3
cellular anatomical structure	2
phosphate-containing compound metabolic process	1
dephosphorylation	1
protein modification process	1
phosphoric ester hydrolase activity	1
phosphatase activity	1
catalytic activity, acting on a protein	1
catalytic activity	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

2 interactions, top by confidence:

A	B	Type	Score
DUSP13A	PCNA	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (114): DUSP13 (Two-hybrid), DUSP13 (Two-hybrid), CALCOCO1 (Two-hybrid), CARD9 (Two-hybrid), DUSP13 (Two-hybrid), NAGLU (Affinity Capture-MS), NUP98 (Proximity Label-MS), NUP107 (Proximity Label-MS), RPGRIP1L (Proximity Label-MS), DUSP13 (Affinity Capture-MS), DUSP13 (Affinity Capture-MS), DCTPP1 (Affinity Capture-MS), HLA-DRB5 (Affinity Capture-MS), KCTD6 (Affinity Capture-MS), ISCA2 (Affinity Capture-MS)

ESM2 similar proteins: A1A4L8, A2BDX3, A5A779, A5GFZ6, A6QQ74, O54838, O60294, P0DPD7, P28562, P28563, Q05922, Q05923, Q08DH8, Q13115, Q16690, Q16829, Q17QJ3, Q1JPJ9, Q2KJ24, Q561R2, Q5FVI9, Q5NVK5, Q5R6H6, Q62767, Q63340, Q64623, Q6B8I0, Q6B8I1, Q6P5Z2, Q6PAT0, Q86U10, Q8BFV3, Q8BGL1, Q8K045, Q8K2J0, Q8K4F6, Q8N3E9, Q8VCZ9, Q90W58, Q91790

Diamond homologs: A0A7H0DN78, P07239, P0C597, P0C598, P0C5A0, P0C5A1, P0DOQ5, P0DOQ6, P20495, P28191, P28562, P28563, P29074, P51452, P80994, Q05923, Q13115, Q16690, Q16828, Q2KJ36, Q4RQD3, Q54R42, Q54T76, Q5RD73, Q62767, Q64346, Q64623, Q6B8I0, Q6B8I1, Q84JU4, Q85297, Q8BFV3, Q90W58, Q91790, Q99956, Q9D0T2, Q9DBB1, Q9J592, Q9M8K7, Q9PW71

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

3 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
147477	GRCh38/hg38 10q21.3-22.2(chr10:63402579-75296099)x1	Pathogenic

SpliceAI

484 predictions. Top by Δscore:

Variant	Effect	Δscore
10:75095569:GTGCA:G	donor_loss	1.0000
10:75095570:TGCAC:T	donor_loss	1.0000
10:75095572:CA:C	donor_loss	1.0000
10:75095573:ACCT:A	donor_loss	1.0000
10:75095574:C:A	donor_loss	1.0000
10:75095791:CGTAC:C	acceptor_gain	1.0000
10:75095792:GTAC:G	acceptor_gain	1.0000
10:75095793:TAC:T	acceptor_gain	1.0000
10:75095794:AC:A	acceptor_gain	1.0000
10:75095795:CC:C	acceptor_gain	1.0000
10:75095796:C:CC	acceptor_gain	1.0000
10:75097706:A:AC	donor_gain	1.0000
10:75097707:C:CC	donor_gain	1.0000
10:75097707:CT:C	donor_gain	1.0000
10:75097707:CTCA:C	donor_gain	1.0000
10:75097710:A:AC	donor_gain	1.0000
10:75097711:C:CA	donor_gain	1.0000
10:75097711:CG:C	donor_gain	1.0000
10:75097711:CGCAT:C	donor_gain	1.0000
10:75094875:CGGC:C	acceptor_gain	0.9900
10:75094876:GGCCT:G	acceptor_loss	0.9900
10:75094878:CCTG:C	acceptor_loss	0.9900
10:75094879:C:CC	acceptor_gain	0.9900
10:75094879:CTGTA:C	acceptor_loss	0.9900
10:75094880:T:G	acceptor_loss	0.9900
10:75095575:C:G	donor_loss	0.9900
10:75095630:A:AC	donor_gain	0.9900
10:75095631:C:CC	donor_gain	0.9900
10:75095796:C:T	acceptor_gain	0.9900
10:75097704:TTAC:T	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.