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    CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 [ Homo sapiens (human) ]

    Gene ID: 26505, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CNNM3provided by HGNC
    Official Full Name
    cyclin and CBS domain divalent metal cation transport mediator 3provided by HGNC
    Primary source
    HGNC:HGNC:104
    See related
    Ensembl:ENSG00000168763 MIM:607804; AllianceGenome:HGNC:104
    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
    ACDP3
    Summary
    Predicted to enable transmembrane transporter activity. Predicted to be involved in magnesium ion homeostasis; monoatomic ion transport; and transmembrane transport. Located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in duodenum (RPKM 7.6), small intestine (RPKM 6.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CNNM3 in Genome Data Viewer
    Location:
    2q11.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (96816268..96837466)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (97322898..97344098)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (97482005..97501119)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene cyclin and CBS domain divalent metal cation transport mediator 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16232 Neighboring gene microRNA 3127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11778 Neighboring gene CNNM3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97494389-97494889 Neighboring gene uncharacterized LOC124907859 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:97498033-97499232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97503062-97503618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97503619-97504173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97507205-97507810 Neighboring gene ankyrin repeat domain 23 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:97510949-97511138 Neighboring gene ankyrin repeat domain 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11782

    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. CNN3 in glioma: The prognostic factor and a potential immunotherapeutic target. Xu H, et al. Medicine (Baltimore), 2021 Nov 19. PMID 34797350, Free PMC Article
    2. The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg(2+) efflux activity. Chen YS, et al. J Biol Chem, 2018 Dec 28. PMID 30341174, Free PMC Article
    3. A FRET-based screening method to detect potential inhibitors of the binding of CNNM3 to PRL2. Cai F, et al. Sci Rep, 2020 Jul 30. PMID 32733084, Free PMC Article
    4. CNNM proteins selectively bind to the TRPM7 channel to stimulate divalent cation entry into cells. Bai Z, et al. PLoS Biol, 2021 Dec. PMID 34928937, Free PMC Article
    5. Molecular cloning and characterization of a novel gene family of four ancient conserved domain proteins (ACDP). Wang CY, et al. Gene, 2003 Mar 13. PMID 12657465

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CNN3 in glioma: The prognostic factor and a potential immunotherapeutic target.
      Title: CNN3 in glioma: The prognostic factor and a potential immunotherapeutic target.
    2. CNNM proteins selectively bind to the TRPM7 channel to stimulate divalent cation entry into cells.
      Title: CNNM proteins selectively bind to the TRPM7 channel to stimulate divalent cation entry into cells.
    3. A FRET-based screening method to detect potential inhibitors of the binding of CNNM3 to PRL2.
      Title: A FRET-based screening method to detect potential inhibitors of the binding of CNNM3 to PRL2.
    4. This study determined the first crystal structures of the cyclic nucleotide-binding homology (CNBH) domain domains of CNNM2 and CNNM3 at 2.6 and 1.9 A resolutions.
      Title: The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg(2+) efflux activity.
    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 to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer.
    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

    • FLJ20018, DKFZp434I1016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in magnesium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in magnesium ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    metal transporter CNNM3
    Names
    ancient conserved domain protein 3
    ancient conserved domain-containing protein 3
    cyclin-M3

    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_017623.5 → NP_060093.3  metal transporter CNNM3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_060093.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC092636, AK126847
      Consensus CDS
      CCDS2025.1
      UniProtKB/Swiss-Prot
      B3KX67, Q8NE01, Q8TBV4, Q96IW4, Q9NRK4, Q9NXW6
      Related
      ENSP00000305449.3, ENST00000305510.4
      Conserved Domains (1) summary
      cd04590
      Location:313 → 442
      CBS_pair_CorC_HlyC_assoc; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains the majority of which are associated with the CorC_HlyC domain

    2. NM_199078.3 → NP_951060.1  metal transporter CNNM3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_951060.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC092636, AK126847, BC007199
      Consensus CDS
      CCDS2026.1
      UniProtKB/Swiss-Prot
      Q8NE01
      Related
      ENSP00000366260.3, ENST00000377060.7
      Conserved Domains (1) summary
      cd04590
      Location:323 → 408
      CBS_pair_CorC_HlyC_assoc; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      96816268..96837466
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510957.4 → XP_011509259.1  metal transporter CNNM3 isoform X2

      Conserved Domains (2) summary
      COG1253
      Location:221 → 467
      TlyC; Hemolysin or related protein, contains CBS domains [General function prediction only]
      cd04590
      Location:323 → 443
      CBS_pair_CorC_HlyC_assoc; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in ...

    2. XM_047443917.1 → XP_047299873.1  metal transporter CNNM3 isoform X6

    3. XM_047443913.1 → XP_047299869.1  metal transporter CNNM3 isoform X1

    4. XM_017003800.3 → XP_016859289.1  metal transporter CNNM3 isoform X3

    5. XM_047443915.1 → XP_047299871.1  metal transporter CNNM3 isoform X5

    6. XM_047443914.1 → XP_047299870.1  metal transporter CNNM3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      97322898..97344098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341370.1 → XP_054197345.1  metal transporter CNNM3 isoform X2

    2. XM_054341374.1 → XP_054197349.1  metal transporter CNNM3 isoform X6

    3. XM_054341369.1 → XP_054197344.1  metal transporter CNNM3 isoform X1

    4. XM_054341371.1 → XP_054197346.1  metal transporter CNNM3 isoform X3

    5. XM_054341373.1 → XP_054197348.1  metal transporter CNNM3 isoform X5

    6. XM_054341372.1 → XP_054197347.1  metal transporter CNNM3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NE01.1 GenPept UniProtKB/Swiss-Prot:Q8NE01

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