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    C12orf43 chromosome 12 open reading frame 43 [ Homo sapiens (human) ]

    Gene ID: 64897, updated on 3-Apr-2024

    Summary

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    Official Symbol
    C12orf43provided by HGNC
    Official Full Name
    chromosome 12 open reading frame 43provided by HGNC
    Primary source
    HGNC:HGNC:25719
    See related
    Ensembl:ENSG00000157895 AllianceGenome:HGNC:25719
    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
    Custos
    Summary
    Predicted to be involved in Spemann organizer formation and negative regulation of Wnt signaling pathway. Predicted to be located in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in kidney (RPKM 7.1), small intestine (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q24.31
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121000486..121016487, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (120990099..121006081, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (121438289..121454290, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:121362870-121364069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:121364035-121364584 Neighboring gene ribosomal protein L12 pseudogene 33 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:121366435-121367242 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:121410688-121411215 Neighboring gene HNF1A antisense RNA 1 Neighboring gene HNF1 homeobox A Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:121453469-121453984 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:121454193-121454386 Neighboring gene 2'-5'-oligoadenylate synthetase like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:121476213-121476714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:121476715-121477214 Neighboring gene Sharpr-MPRA regulatory region 13012 Neighboring gene uncharacterized LOC105378258 Neighboring gene 2'-5' oligoadenylate synthetase like 2, 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. A Single-Nucleotide Polymorphism in C12orf43 Region is Associated with the Risk of Coronary Artery Disease in a Pakistani Cohort. Shahzadi S, et al. Biochem Genet, 2016 Oct. PMID 27263109
    2. New susceptibility locus for coronary artery disease on chromosome 3q22.3. Erdmann J, et al. Nat Genet, 2009 Mar. PMID 19198612, Free PMC Article
    3. New variants including ARG1 polymorphisms associated with C-reactive protein levels identified by genome-wide association and pathway analysis. Vinayagamoorthy N, et al. PLoS One, 2014. PMID 24763700, Free PMC Article
    4. Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation. Lauc G, et al. PLoS Genet, 2010 Dec 23. PMID 21203500, Free PMC Article
    5. Custos controls β-catenin to regulate head development during vertebrate embryogenesis. Komiya Y, et al. Proc Natl Acad Sci U S A, 2014 Sep 9. PMID 25157132, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of a single-nucleotide polymorphism in C12orf43 region with the risk of coronary artery disease.
      Title: Association of a single-nucleotide polymorphism in C12orf43 region with the risk of coronary artery disease.
    2. Study provides evidence that C12orf43/rs2258287 was associated with the risk of coronary artery disease in the studied Pakistani cohort.
      Title: A Single-Nucleotide Polymorphism in C12orf43 Region is Associated with the Risk of Coronary Artery Disease in a Pakistani Cohort.
    3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: New susceptibility locus for coronary artery disease on chromosome 3q22.3.
    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
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog
    Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
    EBI GWAS Catalog
    Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation.
    EBI GWAS Catalog
    New susceptibility locus for coronary artery disease on chromosome 3q22.3.
    EBI GWAS Catalog
    New variants including ARG1 polymorphisms associated with C-reactive protein levels identified by genome-wide association and pathway analysis.
    EBI GWAS Catalog
    Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
    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

    • FLJ12448

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Spemann organizer formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein CUSTOS
    Names
    uncharacterized protein C12orf43

    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_001286191.2 → NP_001273120.1  protein CUSTOS isoform a

      See identical proteins and their annotated locations for NP_001273120.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC079602, AK301566, AK307971, BC014661, BP201132
      Consensus CDS
      CCDS76613.1
      UniProtKB/TrEMBL
      B4DWJ9, F5H7W8
      Related
      ENSP00000442224.2, ENST00000537817.5

    2. NM_001286192.2 → NP_001273121.1  protein CUSTOS isoform b

      See identical proteins and their annotated locations for NP_001273121.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses alternate splice sites at two coding exons, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC079602, AK225162, AK307971, BC014661, BP201132
      UniProtKB/TrEMBL
      B4DWJ9

    3. NM_001286195.2 → NP_001273124.1  protein CUSTOS isoform d

      See identical proteins and their annotated locations for NP_001273124.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses alternate splice sites at three coding exons, but maintains the reading frame, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AC079602, AK301566, BC014661
      Consensus CDS
      CCDS66487.1
      UniProtKB/TrEMBL
      B4DWJ9, G5EA44
      Related
      ENSP00000437803.1, ENST00000539736.5

    4. NM_001286196.2 → NP_001273125.1  protein CUSTOS isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses alternate splice sites at two coding exons, but maintains the reading frame, compared to variant 1. The encoded isoform (e) is shorter than isoform a.
      Source sequence(s)
      AC079602, AK301566, AK307971, BC014661, BP201132, DC297725
      UniProtKB/TrEMBL
      B4DWJ9

    5. NM_001286197.2 → NP_001273126.1  protein CUSTOS isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an exon and uses alternate splice sites at two coding exons, but maintains the reading frame, compared to variant 1. The encoded isoform (f) is shorter than isoform a.
      Source sequence(s)
      AC079602, AK307971, BC014661, BP201132, BP343829
      UniProtKB/TrEMBL
      F5H8B7
      Related
      ENSP00000442041.2, ENST00000538296.5

    6. NM_001286198.2 → NP_001273127.1  protein CUSTOS isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) contains an alternate exon and uses alternate splice sites at two coding exons, compared to variant 1. It initiates translation at an alternate start codon. The encoded isoform (g) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AC079602, AK225162, AK299170, AK307971, BC014661, BP201132
      Consensus CDS
      CCDS66486.1
      UniProtKB/TrEMBL
      B4DRA4, E7ENF1
      Related
      ENSP00000409788.3, ENST00000445832.7

    7. NM_022895.3 → NP_075046.1  protein CUSTOS isoform c

      See identical proteins and their annotated locations for NP_075046.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site at a coding exon, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC079602, AK022510, AK301566, AK307971, BC014661, BP201132
      Consensus CDS
      CCDS9210.1
      UniProtKB/Swiss-Prot
      Q53HF0, Q96C57, Q9H9Z7
      UniProtKB/TrEMBL
      B4DWJ9
      Related
      ENSP00000288757.5, ENST00000288757.7

    RNA

    1. NR_104409.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) uses alternate splice sites at three internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC079602, AK301566, BC014661, DA014862

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      121000486..121016487 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019829.3 → XP_016875318.1  protein CUSTOS isoform X1

      UniProtKB/TrEMBL
      B4DRA4

    2. XM_047429368.1 → XP_047285324.1  protein CUSTOS isoform X2

      Related
      ENSP00000438856.1, ENST00000535367.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      120990099..121006081 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372920.1 → XP_054228895.1  protein CUSTOS isoform X1

    2. XM_054372921.1 → XP_054228896.1  protein CUSTOS isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96C57.2 GenPept UniProtKB/Swiss-Prot:Q96C57

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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