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    MINDY3 MINDY lysine 48 deubiquitinase 3 [ Homo sapiens (human) ]

    Gene ID: 80013, updated on 29-Oct-2024

    Summary

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    Official Symbol
    MINDY3provided by HGNC
    Official Full Name
    MINDY lysine 48 deubiquitinase 3provided by HGNC
    Primary source
    HGNC:HGNC:23578
    See related
    Ensembl:ENSG00000148481 MIM:611649; AllianceGenome:HGNC:23578
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CARP; DERP5; my042; MST126; FAM188A; MSTP126; C10orf97
    Summary
    The protein encoded by this gene contains a caspase-associated recruitment domain and may function in apoptosis. It has been identified as a tumor suppressor in lung and gastric cancers, and a polymorphism in the gene may be associated with gastric cancer risk. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 5.8), adrenal (RPKM 4.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MINDY3 in Genome Data Viewer
    Location:
    10p13
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (15778174..15860507, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (15796178..15878518, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (15820173..15902506, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15290229-15290730 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:15297713-15298356 Neighboring gene family with sequence similarity 171 member A1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15310079-15310579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3094 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:15366997-15368196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2173 Neighboring gene Sharpr-MPRA regulatory region 1502 Neighboring gene MPRA-validated peak874 silencer Neighboring gene Sharpr-MPRA regulatory region 6046 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:15514928-15515649 Neighboring gene MPRA-validated peak875 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2174 Neighboring gene integrin subunit alpha 8 Neighboring gene Sharpr-MPRA regulatory region 12763 Neighboring gene Sharpr-MPRA regulatory region 7083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15731307-15731808 Neighboring gene MPRA-validated peak877 silencer Neighboring gene uncharacterized LOC124902383 Neighboring gene MPRA-validated peak878 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3096 Neighboring gene Sharpr-MPRA regulatory region 8556 Neighboring gene small nucleolar RNA U13 Neighboring gene ferritin light chain pseudogene 19

    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 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. CARP is a novel caspase recruitment domain containing pro-apoptotic protein. Liu B, et al. Biochem Biophys Res Commun, 2002 May 24. PMID 12054670
    2. Genome-wide mapping of modifier chromosomal loci for human hypertrophic cardiomyopathy. Daw EW, et al. Hum Mol Genet, 2007 Oct 15. PMID 17652099, Free PMC Article
    3. CARP is a potential tumor suppressor in gastric carcinoma and a single-nucleotide polymorphism in CARP gene might increase the risk of gastric carcinoma. Lu F, et al. PLoS One, 2014. PMID 24870804, Free PMC Article
    4. C10ORF97 is a novel tumor-suppressor gene of non-small-cell lung cancer and a functional variant of this gene increases the risk of non-small-cell lung cancer. Shi Y, et al. Oncogene, 2011 Sep 29. PMID 21499297
    5. CircFAM188A Regulates Autophagy via miR-670-3p and ULK1 in Epithelial Ovarian Carcinoma. Yong M, et al. Cancer Rep (Hoboken), 2024 Sep. PMID 39229655, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircFAM188A Regulates Autophagy via miR-670-3p and ULK1 in Epithelial Ovarian Carcinoma.
      Title: CircFAM188A Regulates Autophagy via miR-670-3p and ULK1 in Epithelial Ovarian Carcinoma.
    2. CARP is a potential tumor suppressor of gastric carcinoma and the rs2297882 C>T phenotype of CARP may serve as a predictor of gastric carcinoma.
      Title: CARP is a potential tumor suppressor in gastric carcinoma and a single-nucleotide polymorphism in CARP gene might increase the risk of gastric carcinoma.
    3. results indicated that C10ORF97 functions as a novel tumor suppressor by modulating several key G(1)/S-regulatory proteins by interacting with JAB1
      Title: C10ORF97 is a novel tumor-suppressor gene of non-small-cell lung cancer and a functional variant of this gene increases the risk of non-small-cell lung cancer.
    4. CARP is a novel caspase recruitment domain containing pro-apoptotic protein. (CARP, CARD containing Protein)
      Title: CARP is a novel caspase recruitment domain containing pro-apoptotic protein.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    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

    Clone Names

    • FLJ13397

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K48-linked deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K48-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein K48-linked deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase MINDY-3
    Names
    CARD-containing protein
    MINDY deubiquitinase 3
    caspase recruitment domain containing pro-apoptotic protein
    dermal papilla-derived protein 5
    deubiquitinating enzyme MINDY-3
    family with sequence similarity 188 member A
    protein FAM188A
    ubiquitin carboxyl-terminal hydrolase FAM188A
    NP_001305259.1
    NP_079224.1
    XP_005252657.1
    XP_006717571.1
    XP_011517992.1
    XP_011517993.1
    XP_011517996.1
    XP_016872160.1
    XP_047281728.1
    XP_047281729.1
    XP_047281730.1
    XP_047281731.1
    XP_047281732.1
    XP_054222749.1
    XP_054222750.1
    XP_054222751.1
    XP_054222752.1
    XP_054222753.1
    XP_054222754.1
    XP_054222755.1
    XP_054222756.1
    XP_054222757.1
    XP_054222758.1
    XP_054222759.1

    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_001318330.2 → NP_001305259.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform (a).
      Source sequence(s)
      AI573091, AK023459, BC020605, DA063140
      UniProtKB/Swiss-Prot
      Q9H8M7
      Related
      ENST00000477891.1
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    2. NM_024948.4 → NP_079224.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform a

      See identical proteins and their annotated locations for NP_079224.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI573091, AK023459, DA063140
      Consensus CDS
      CCDS7110.1
      UniProtKB/Swiss-Prot
      Q5SZ68, Q5SZ69, Q5SZ70, Q6IA40, Q6P7P0, Q7Z2S1, Q8WUF1, Q9H3I4, Q9H8M7
      Related
      ENSP00000277632.3, ENST00000277632.8
      Conserved Domains (1) summary
      pfam13898
      Location:29 → 315
      DUF4205; Domain of unknown function (DUF4205)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      15778174..15860507 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005252600.3 → XP_005252657.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

      See identical proteins and their annotated locations for XP_005252657.1

      UniProtKB/Swiss-Prot
      Q9H8M7
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    2. XM_006717508.3 → XP_006717571.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X2

      See identical proteins and their annotated locations for XP_006717571.1

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 267
      DUF4205; Domain of unknown function (DUF4205)

    3. XM_011519694.2 → XP_011517996.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

      See identical proteins and their annotated locations for XP_011517996.1

      UniProtKB/Swiss-Prot
      Q9H8M7
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    4. XM_047425774.1 → XP_047281730.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X8

    5. XM_047425773.1 → XP_047281729.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X6

    6. XM_017016671.2 → XP_016872160.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X3

    7. XM_011519690.3 → XP_011517992.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X1

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 315
      DUF4205; Domain of unknown function (DUF4205)

    8. XM_047425772.1 → XP_047281728.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X5

    9. XM_011519691.3 → XP_011517993.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X4

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 315
      DUF4205; Domain of unknown function (DUF4205)

    10. XM_047425776.1 → XP_047281732.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X10

    11. XM_047425775.1 → XP_047281731.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      15796178..15878518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366781.1 → XP_054222756.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

    2. XM_054366775.1 → XP_054222750.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X2

    3. XM_054366780.1 → XP_054222755.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

    4. XM_054366782.1 → XP_054222757.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X8

    5. XM_054366779.1 → XP_054222754.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X6

    6. XM_054366776.1 → XP_054222751.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X3

    7. XM_054366774.1 → XP_054222749.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X1

    8. XM_054366778.1 → XP_054222753.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X5

    9. XM_054366777.1 → XP_054222752.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X4

    10. XM_054366784.1 → XP_054222759.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X10

    11. XM_054366783.1 → XP_054222758.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H8M7.1 GenPept UniProtKB/Swiss-Prot:Q9H8M7

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