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

Gene ID: 64897, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in kidney (RPKM 7.1), small intestine (RPKM 5.6) and 25 other tissues See more
Orthologs
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Genomic context

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See C12orf43 in Genome Data Viewer
Location:
12q24.31
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121000486..121016487, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (120990099..121006081, complement)
RS_2024_09 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 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. Association of a single-nucleotide polymorphism in C12orf43 region with the risk of coronary artery disease. Qammar N, et al. Cell Mol Biol (Noisy-le-grand), 2024 Feb 29. PMID 38430045
  2. 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
  3. New susceptibility locus for coronary artery disease on chromosome 3q22.3. Erdmann J, et al. Nat Genet, 2009 Mar. PMID 19198612, Free PMC Article
  4. 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
  5. 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

See all (41) 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_2024_08

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

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