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STYXL1 serine/threonine/tyrosine interacting like 1 [ Homo sapiens (human) ]

Gene ID: 51657, updated on 7-Apr-2024

Summary

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Official Symbol
STYXL1provided by HGNC
Official Full Name
serine/threonine/tyrosine interacting like 1provided by HGNC
Primary source
HGNC:HGNC:18165
See related
Ensembl:ENSG00000127952 MIM:616695; AllianceGenome:HGNC:18165
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DUSP24; MKSTYX; MK-STYX
Summary
Enables protein phosphatase binding activity; protein phosphatase inhibitor activity; and pseudophosphatase activity. Involved in several processes, including negative regulation of phosphoprotein phosphatase activity; negative regulation of stress granule assembly; and positive regulation of intrinsic apoptotic signaling pathway. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 9.4), esophagus (RPKM 5.9) and 25 other tissues See more
Orthologs
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Genomic context

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See STYXL1 in Genome Data Viewer
Location:
7q11.23
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (75996337..76048000, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (77283904..77335536, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (75625655..75677318, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene cytochrome p450 oxidoreductase Neighboring gene small nucleolar RNA, H/ACA box 14A Neighboring gene Sharpr-MPRA regulatory region 2709 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75596037-75596916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:75612087-75613286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26186 Neighboring gene Sharpr-MPRA regulatory region 3792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18303 Neighboring gene transmembrane protein 120A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75630123-75630623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26188 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75648513-75649014 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75676791-75677573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75677574-75678355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26192 Neighboring gene malate dehydrogenase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75700542-75701066 Neighboring gene RNA, U6 small nuclear 863, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Pseudophosphatase STYXL1 depletion enhances glucocerebrosidase trafficking to lysosomes via ER stress. Patel S, et al. Traffic, 2023 Jul. PMID 37198709
  2. Serine/threonine/tyrosine-interacting-like protein 1 (STYXL1), a pseudo phosphatase, promotes oncogenesis in glioma. Tomar VS, et al. Biochem Biophys Res Commun, 2019 Jul 12. PMID 31146910
  3. Pseudophosphatase MK-STYX Alters Histone Deacetylase 6 Cytoplasmic Localization, Decreases Its Phosphorylation, and Increases Detyrosination of Tubulin. Cao Y, et al. Int J Mol Sci, 2019 Mar 22. PMID 30909412, Free PMC Article
  4. A previously identified missense mutation in STYXL1 is likely benign. Hengel H, et al. Eur J Med Genet, 2019 Nov. PMID 30472486
  5. Homozygous missense mutation in STYXL1 associated with moderate intellectual disability, epilepsy and behavioural complexities. Isrie M, et al. Eur J Med Genet, 2015 Apr. PMID 25724587

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The DUSP domain of pseudophosphatase MK-STYX interacts with G3BP1 to decrease stress granules.
    Title: The DUSP domain of pseudophosphatase MK-STYX interacts with G3BP1 to decrease stress granules.
  2. Pseudophosphatase STYXL1 depletion enhances glucocerebrosidase trafficking to lysosomes via ER stress.
    Title: Pseudophosphatase STYXL1 depletion enhances glucocerebrosidase trafficking to lysosomes via ER stress.
  3. STYXL1 promotes malignant progression of hepatocellular carcinoma via downregulating CELF2 through the PI3K/Akt pathway.
    Title: STYXL1 promotes malignant progression of hepatocellular carcinoma via downregulating CELF2 through the PI3K/Akt pathway.
  4. Silencing serine/threonine/tyrosine-interacting-like protein 1 (STYXL1) inhibited glioma cell growth, soft agar colony formation, migration, invasion, proliferation, and xenograft tumor growth [Review].
    Title: Serine/threonine/tyrosine-interacting-like protein 1 (STYXL1), a pseudo phosphatase, promotes oncogenesis in glioma.
  5. We have detected this variant via whole exome sequencing in a homozygous state in two families. Segregation analyses in our families and thorough validation in international genetic databases provides evidence that this variant is most likely benign. This is important information for genetic counselling. The role of STYXL1 variants in human disease needs to be established
    Title: A previously identified missense mutation in STYXL1 is likely benign.
  6. These findings show that MK-STYX decreases the number of HDAC6-containing aggregates and alters their localization, sustains microtubule acetylation, and increases detyrosination of microtubules, implicating MK-STYX as a signaling molecule in HDAC6 activity.
    Title: Pseudophosphatase MK-STYX Alters Histone Deacetylase 6 Cytoplasmic Localization, Decreases Its Phosphorylation, and Increases Detyrosination of Tubulin.
  7. this study revealed STYXL1 as a novel candidate gene for moderate intellectual disability, seizures and behavioral complexities.
    Title: Homozygous missense mutation in STYXL1 associated with moderate intellectual disability, epilepsy and behavioural complexities.
  8. our data support a model in which MK-STYX controls apoptosis by negatively regulating PTPMT1.
    Title: The pseudophosphatase MK-STYX physically and genetically interacts with the mitochondrial phosphatase PTPMT1.
  9. The pseudophosphatase MK-STYX plays a key role in the cellular response to stress.
    Title: The pseudophosphatase MK-STYX inhibits stress granule assembly independently of Ser149 phosphorylation of G3BP-1.
  10. MK-STYX regulates mitochondrial outer membrane permeabilization using a distinct mechanism.
    Title: MK-STYX, a catalytically inactive phosphatase regulating mitochondrially dependent apoptosis.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein phosphatase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein phosphatase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein phosphatase inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein phosphatase inhibitor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein tyrosine/serine/threonine phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables pseudophosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pseudophosphatase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of phosphoprotein phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of stress granule assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of stress granule assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of intrinsic apoptotic signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of intrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of intrinsic apoptotic signaling pathway IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
serine/threonine/tyrosine-interacting-like protein 1
Names
dual specificity phosphatase 24 (putative)
dual specificity phosphatase inhibitor MK-STYX
dual specificity protein phosphatase 24
inactive dual specificity protein phosphatase MK-STYX
map kinase phosphatase-like protein MK-STYX

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001317785.2 → NP_001304714.1  serine/threonine/tyrosine-interacting-like protein 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).
    Source sequence(s)
    AC006330, AF069762, BC024035, BM824947, BM972220
    Consensus CDS
    CCDS5580.1
    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8
    UniProtKB/TrEMBL
    C9J4H0
    Related
    ENSP00000352726.3, ENST00000359697.8
    Conserved Domains (2) summary
    pfam00581
    Location:22 → 135
    Rhodanese; Rhodanese-like domain
    cl21483
    Location:160 → 297
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  2. NM_001317786.2 → NP_001304715.1  serine/threonine/tyrosine-interacting-like protein 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).
    Source sequence(s)
    AC006330, AF069762, AL533027, BX537896
    Consensus CDS
    CCDS5580.1
    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8
    UniProtKB/TrEMBL
    C9J4H0
    Related
    ENSP00000392221.1, ENST00000431581.5
    Conserved Domains (2) summary
    pfam00581
    Location:22 → 135
    Rhodanese; Rhodanese-like domain
    cl21483
    Location:160 → 297
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  3. NM_001317787.2 → NP_001304716.1  serine/threonine/tyrosine-interacting-like protein 1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' UTR, and lacks two consecutive in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform 1.
    Source sequence(s)
    AC006330, AF069762, BX537896
    Consensus CDS
    CCDS83193.1
    UniProtKB/TrEMBL
    Q7Z3H6
    Related
    ENSP00000343383.5, ENST00000340062.9
    Conserved Domains (2) summary
    cl00125
    Location:23 → 51
    RHOD; Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins ...
    cl21483
    Location:64 → 201
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  4. NM_001317788.2 → NP_001304717.1  serine/threonine/tyrosine-interacting-like protein 1 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two exons in the 5' coding region, and uses an alternate splice site in the 3'coding region which results in a frameshift, compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC006330, AF069762, BM972220, BU859937
    UniProtKB/Swiss-Prot
    Q9Y6J8
    Conserved Domains (2) summary
    cl00125
    Location:23 → 51
    RHOD; Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins ...
    cl21483
    Location:64 → 129
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  5. NM_001317789.1 → NP_001304718.1  serine/threonine/tyrosine-interacting-like protein 1 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in its 5' UTR, lacks an exon in the 5' coding region, and uses an alternate downstream start codon which results in a frameshift, compared to variant 1. The encoded isoform (d) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF188204, BM126964, BM972220, BX537896
    UniProtKB/Swiss-Prot
    Q9Y6J8
    UniProtKB/TrEMBL
    Q7Z3H6
    Conserved Domains (1) summary
    cl21483
    Location:22 → 159
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  6. NM_016086.3 → NP_057170.1  serine/threonine/tyrosine-interacting-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_057170.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform (a). Variants 1, 2, and 3 encode the same isoform (a).
    Source sequence(s)
    AA782050, AF069762, BC024035, BM824947
    Consensus CDS
    CCDS5580.1
    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8
    UniProtKB/TrEMBL
    C9J4H0
    Related
    ENSP00000248600.1, ENST00000248600.5
    Conserved Domains (2) summary
    pfam00581
    Location:22 → 135
    Rhodanese; Rhodanese-like domain
    cl21483
    Location:160 → 297
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

RNA

  1. NR_134486.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site in the 5'-terminal exon and lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AF069762, AY927581, BI772699, BM972220

  2. NR_134487.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) lacks two exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AF188201, BM126964, BM972220

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    75996337..76048000 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516293.4 → XP_011514595.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011514595.1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8
    UniProtKB/TrEMBL
    C9J4H0
    Related
    ENSP00000411812.1, ENST00000451157.1
    Conserved Domains (2) summary
    pfam00581
    Location:22 → 135
    Rhodanese; Rhodanese-like domain
    cl21483
    Location:160 → 297
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  2. XM_047420470.1 → XP_047276426.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X2

  3. XM_047420466.1 → XP_047276422.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  4. XM_047420468.1 → XP_047276424.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  5. XM_047420467.1 → XP_047276423.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  6. XM_047420469.1 → XP_047276425.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    77283904..77335536 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358387.1 → XP_054214362.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X3

  2. XM_054358382.1 → XP_054214357.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  3. XM_054358388.1 → XP_054214363.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X2

  4. XM_054358384.1 → XP_054214359.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  5. XM_054358385.1 → XP_054214360.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  6. XM_054358383.1 → XP_054214358.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8

  7. XM_054358386.1 → XP_054214361.1  serine/threonine/tyrosine-interacting-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBP1, Q9UK06, Q9UK07, Q9UKG2, Q9UKG3, Q9Y6J8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y6J8.1 GenPept UniProtKB/Swiss-Prot:Q9Y6J8

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