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    C2CD2 C2 calcium dependent domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 25966, updated on 3-Nov-2024

    Summary

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    Official Symbol
    C2CD2provided by HGNC
    Official Full Name
    C2 calcium dependent domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:1266
    See related
    Ensembl:ENSG00000157617 MIM:617581; AllianceGenome:HGNC:1266
    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
    TMEM24L; C21orf25; C21orf258
    Summary
    Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in adrenal (RPKM 38.9), fat (RPKM 23.4) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C2CD2 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41885112..41954018, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40275427..40344241, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43305221..43374127, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724800 Neighboring gene Sharpr-MPRA regulatory region 172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43192149-43192696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:43216480-43216980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18485 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43241376-43242575 Neighboring gene PR/SET domain 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43256373-43257080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43274198-43275397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43318691-43319691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43364315-43364815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43370715-43371220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43373099-43373873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43378985-43379952 Neighboring gene small nucleolar RNA, H/ACA box 91 Neighboring gene NANOG hESC enhancer GRCh37_chr21:43388567-43389068 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:43415728-43415930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13337 Neighboring gene zinc finger and BTB domain containing 21 Neighboring gene ZNF295 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43460101-43460604 Neighboring gene uncharacterized LOC107985502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43461111-43461614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43463997-43464496

    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. A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts. Johnson B, et al. J Cell Biol, 2024 Nov 4. PMID 39158698, Free PMC Article
    2. Genetic variants associated with physical performance and anthropometry in old age: a genome-wide association study in the ilSIRENTE cohort. Heckerman D, et al. Sci Rep, 2017 Nov 20. PMID 29158487, Free PMC Article
    3. Identification and characterization of TMEM24 family genes in silico. Katoh M, et al. Int J Oncol, 2004 Sep. PMID 15289880
    4. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Chimusa ER, et al. Hum Mol Genet, 2014 Feb 1. PMID 24057671, Free PMC Article
    5. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Warnatz HJ, et al. Nucleic Acids Res, 2010 Oct. PMID 20494980, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts.
      Title: A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts.
    2. Genotyping was accomplished on Infinium Human610-QUAD version 1. In the ilSIRENTE population, genetic variants in ZNF295 and C2CD2 (rs928874 and rs1788355) on chromosome 21q22.3, were significantly associated with the 4-meter gait speed
      Title: Genetic variants associated with physical performance and anthropometry in old age: a genome-wide association study in the ilSIRENTE cohort.
    3. The C2CD2/C21orf25 promoter is activated by Trichostatin A (TSA) treatment and by serum depletion according to promoter reporter assays in HEK 293 cells.
      Title: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
    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 ancestry-specific TB risk in the South African Coloured population.
    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

    • MGC71445, DKFZp686O198, DKFZp586F0422

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in cytosol HDA PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    C2 domain-containing protein 2
    Names
    TMEM24 related geme
    transmembrane protein 24-like

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_015500.2 → NP_056315.1  C2 domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_056315.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB047784, AP001619
      Consensus CDS
      CCDS42933.1
      UniProtKB/Swiss-Prot
      Q5R2V7, Q6AHX8, Q9NSE6, Q9Y426
      Related
      ENSP00000369853.3, ENST00000380486.4
      Conserved Domains (1) summary
      cd08678
      Location:265 → 391
      C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

    2. NM_199050.3 → NP_950251.1  C2 domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_950251.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AI143200, AL833323, AP001619
      Consensus CDS
      CCDS13677.1
      UniProtKB/Swiss-Prot
      Q9Y426
      Related
      ENSP00000329302.7, ENST00000329623.11
      Conserved Domains (1) summary
      cd08678
      Location:110 → 236
      C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      41885112..41954018 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529522.3 → XP_011527824.1  C2 domain-containing protein 2 isoform X1

      Conserved Domains (1) summary
      cd08678
      Location:276 → 402
      C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

    2. XM_011529523.3 → XP_011527825.1  C2 domain-containing protein 2 isoform X2

      Conserved Domains (1) summary
      cd08678
      Location:185 → 311
      C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

    3. XM_005261109.5 → XP_005261166.1  C2 domain-containing protein 2 isoform X3

      See identical proteins and their annotated locations for XP_005261166.1

      UniProtKB/Swiss-Prot
      Q9Y426
      Conserved Domains (1) summary
      cd08678
      Location:110 → 236
      C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      40275427..40344241 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324425.1 → XP_054180400.1  C2 domain-containing protein 2 isoform X1

    2. XM_054324426.1 → XP_054180401.1  C2 domain-containing protein 2 isoform X2

    3. XM_054324427.1 → XP_054180402.1  C2 domain-containing protein 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y426.2 GenPept UniProtKB/Swiss-Prot:Q9Y426

    Gene LinkOut

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

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