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    EFCAB13 EF-hand calcium binding domain 13 [ Homo sapiens (human) ]

    Gene ID: 124989, updated on 17-Sep-2024

    Summary

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    Official Symbol
    EFCAB13provided by HGNC
    Official Full Name
    EF-hand calcium binding domain 13provided by HGNC
    Primary source
    HGNC:HGNC:26864
    See related
    Ensembl:ENSG00000178852 AllianceGenome:HGNC:26864
    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
    C17orf57
    Expression
    Broad expression in testis (RPKM 5.5), thyroid (RPKM 2.8) and 21 other tissues See more
    Orthologs
    all
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    Genomic context

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    See EFCAB13 in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47323955..47441312)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48186334..48303979)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (45401321..45518678)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985029 Neighboring gene Sharpr-MPRA regulatory region 4923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12309 Neighboring gene Sharpr-MPRA regulatory region 4395 Neighboring gene VISTA enhancer hs2033 Neighboring gene integrin subunit beta 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45369753-45370253 Neighboring gene EFCAB13 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12311 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:45416653-45417154 Neighboring gene Sharpr-MPRA regulatory region 1659 Neighboring gene UDP-N-acetylglucosamine pyrophosphorylase 1 pseudogene Neighboring gene MPRA-validated peak2872 silencer Neighboring gene MPRA-validated peak2873 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8626 Neighboring gene nuclear factor, erythroid 2 like 3 pseudogene 2 Neighboring gene mitochondrial ribosomal protein L45 pseudogene 2 Neighboring gene MPRA-validated peak2874 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45569915-45570430 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:45579384-45580583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45598943-45599444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8629 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:45614024-45614225 Neighboring gene aminopeptidase puromycin sensitive Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45643631-45644132 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45644133-45644632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45693347-45693848 Neighboring gene KPNB1 divergent transcript

    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. Health and population effects of rare gene knockouts in adult humans with related parents. Narasimhan VM, et al. Science, 2016 Apr 22. PMID 26940866, Free PMC Article
    2. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Saleheen D, et al. Nature, 2017 Apr 12. PMID 28406212, Free PMC Article
    3. Identification of a large set of rare complete human knockouts. Sulem P, et al. Nat Genet, 2015 May. PMID 25807282
    4. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Rausell A, et al. Proc Natl Acad Sci U S A, 2020 Jun 16. PMID 32487729, Free PMC Article
    5. The mutational constraint spectrum quantified from variation in 141,456 humans. Karczewski KJ, et al. Nature, 2020 May. PMID 32461654, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-02)

    ClinGen Genome Curation Page
    Haploinsufficency

    Dosage sensitivity unlikely (Last evaluated 2021-02-02)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    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

    Potential readthrough

    Included gene: ITGB3

    Homology

    Clone Names

    • FLJ36110, FLJ40342, FLJ58126

    General protein information

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    Preferred Names
    EF-hand calcium-binding domain-containing protein 13
    Names
    EF-hand domain-containing protein C17orf57

    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_001195192.2 → NP_001182121.1  EF-hand calcium-binding domain-containing protein 13 isoform B

      See identical proteins and their annotated locations for NP_001182121.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (B) contains an alternate segment in the 3' UTR and lacks two internal in-frame exons and the last exon, compared to variant A. The resulting protein (isoform B) is shorter than isoform A.
      Source sequence(s)
      AC040934, AC068234, BC036407, BC037876, BX471329
      Consensus CDS
      CCDS56034.1
      UniProtKB/Swiss-Prot
      Q8IY85
      Related
      ENSP00000430048.1, ENST00000517484.5
      Conserved Domains (2) summary
      COG5126
      Location:440 → 566
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
      cl08302
      Location:375 → 422
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    2. NM_001426585.1 → NP_001413514.1  EF-hand calcium-binding domain-containing protein 13 isoform C

      Status: VALIDATED

      Source sequence(s)
      AC040934, AC068234

    3. NM_001426586.1 → NP_001413515.1  EF-hand calcium-binding domain-containing protein 13 isoform D

      Status: VALIDATED

      Source sequence(s)
      AC040934, AC068234

    4. NM_001426587.1 → NP_001413516.1  EF-hand calcium-binding domain-containing protein 13 isoform E

      Status: VALIDATED

      Source sequence(s)
      AC040934, AC068234

    5. NM_001426588.1 → NP_001413517.1  EF-hand calcium-binding domain-containing protein 13 isoform F

      Status: VALIDATED

      Source sequence(s)
      AC040934, AC068234

    6. NM_001426589.1 → NP_001413518.1  EF-hand calcium-binding domain-containing protein 13 isoform G

      Status: VALIDATED

      Source sequence(s)
      AC068234

    7. NM_001426590.1 → NP_001413519.1  EF-hand calcium-binding domain-containing protein 13 isoform G

      Status: VALIDATED

      Source sequence(s)
      AC068234

    8. NM_001426591.1 → NP_001413520.1  EF-hand calcium-binding domain-containing protein 13 isoform H

      Status: VALIDATED

      Source sequence(s)
      AC068234

    9. NM_001426592.1 → NP_001413521.1  EF-hand calcium-binding domain-containing protein 13 isoform H

      Status: VALIDATED

      Source sequence(s)
      AC068234

    10. NM_001426593.1 → NP_001413522.1  EF-hand calcium-binding domain-containing protein 13 isoform H

      Status: VALIDATED

      Source sequence(s)
      AC068234

    11. NM_152347.5 → NP_689560.3  EF-hand calcium-binding domain-containing protein 13 isoform A

      See identical proteins and their annotated locations for NP_689560.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A).
      Source sequence(s)
      AC040934, AC068234, BC036407, BX471329
      Consensus CDS
      CCDS11512.1
      UniProtKB/Swiss-Prot
      G3V128, Q49AG9, Q8IY85
      Related
      ENSP00000332111.2, ENST00000331493.7
      Conserved Domains (3) summary
      PTZ00184
      Location:448 → 592
      PTZ00184; calmodulin; Provisional
      COG5126
      Location:536 → 662
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
      cl08302
      Location:471 → 518
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RNA

    1. NR_189741.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CP068261

    2. NR_189742.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CP068261

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      47323955..47441312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      48186334..48303979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IY85.2 GenPept UniProtKB/Swiss-Prot:Q8IY85

    Gene LinkOut

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

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