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

Gene ID: 80013, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (15778174..15860507, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (15796178..15878518, complement)
105.20220307 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
  • 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 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
  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 novel caspase recruitment domain containing pro-apoptotic protein. Liu B, et al. Biochem Biophys Res Commun, 2002 May 24. PMID 12054670
  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. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Abdul Rehman SA, et al. Mol Cell, 2016 Jul 7. PMID 27292798, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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 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_2023_10

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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