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    CACHD1 cache domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 57685, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CACHD1provided by HGNC
    Official Full Name
    cache domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:29314
    See related
    Ensembl:ENSG00000158966 MIM:620144; AllianceGenome:HGNC:29314
    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
    Summary
    Predicted to enable voltage-gated calcium channel activity. Predicted to be involved in calcium ion transmembrane transport. Predicted to be located in membrane. Predicted to be part of voltage-gated calcium channel complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 11.0), adrenal (RPKM 7.8) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CACHD1 in Genome Data Viewer
    Location:
    1p31.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (64470129..64693053)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (64347926..64571142)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (64935812..65158736)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene U7 small nuclear RNA Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:64868467-64869666 Neighboring gene RNA, U7 small nuclear 62 pseudogene Neighboring gene uncharacterized LOC107984966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 955 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:64937941-64938726 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:64938727-64939512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:64959581-64960226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:64970443-64970942 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:64982487-64983302 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:64983303-64984116 Neighboring gene NANOG hESC enhancer GRCh37_chr1:65011650-65012151 Neighboring gene uncharacterized LOC124904195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:65037847-65038552 Neighboring gene microRNA 4794 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:65129441-65129616 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 957 Neighboring gene ribonucleoprotein, PTB binding 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1129 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:65312286-65313485 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:65326691-65327236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1134 Neighboring gene Janus kinase 1 Neighboring gene Sharpr-MPRA regulatory region 6411 Neighboring gene NDUFA4, mitochondrial complex associated 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. CACHD1 is an α2δ-Like Protein That Modulates Ca(V)3 Voltage-Gated Calcium Channel Activity. Cottrell GS, et al. J Neurosci, 2018 Oct 24. PMID 30181139, Free PMC Article
    2. CACHD1: A new activity-modifying protein for voltage-gated calcium channels. Stephens GJ, et al. Channels (Austin), 2019 Dec. PMID 30983497, Free PMC Article
    3. Biallelic loss-of-function variants in CACHD1 cause a novel neurodevelopmental syndrome with facial dysmorphism and multisystem congenital abnormalities. Scala M, et al. Genet Med, 2024 Apr. PMID 38158856
    4. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877
    5. Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. Kim TY, et al. Mol Cell Biol, 2015 Jan. PMID 25332235, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic loss-of-function variants in CACHD1 cause a novel neurodevelopmental syndrome with facial dysmorphism and multisystem congenital abnormalities.
      Title: Biallelic loss-of-function variants in CACHD1 cause a novel neurodevelopmental syndrome with facial dysmorphism and multisystem congenital abnormalities.
    2. CACHD1 increases the presence of CaV3.1 at the cell surface and causes an increase in channel open probability.
      Title: CACHD1 is an α2δ-Like Protein That Modulates Ca(V)3 Voltage-Gated Calcium Channel Activity.
    3. CACHD1: A new activity-modifying protein for voltage-gated calcium channels
      Title: CACHD1: A new activity-modifying protein for voltage-gated calcium channels.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    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

    • KIAA1573

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables voltage-gated calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of voltage-gated calcium channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    VWFA and cache domain-containing protein 1
    Names
    cache domain-containing protein 1
    von Willebrand factor type A and cache domain containing 1

    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_001293274.2 → NP_001280203.1  VWFA and cache domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AK022571, AL355515, AL590405, BC039301, BX537603
      UniProtKB/TrEMBL
      A0A3B3ISH2
      Related
      ENST00000495994.5

    2. NM_020925.4 → NP_065976.3  VWFA and cache domain-containing protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC099678, AL355515, AL590405
      Consensus CDS
      CCDS628.3
      UniProtKB/Swiss-Prot
      Q49AE9, Q5VU97, Q658T4, Q7Z3P2, Q9H7W4, Q9H9W3, Q9HCJ9
      UniProtKB/TrEMBL
      A0A0A0MQY7
      Related
      ENSP00000498498.1, ENST00000651257.2
      Conserved Domains (2) summary
      pfam08399
      Location:95 → 204
      VWA_N; VWA N-terminal
      cl00057
      Location:213 → 408
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      64470129..64693053
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426234.1 → XP_047282190.1  VWFA and cache domain-containing protein 1 isoform X1

    2. XM_047426235.1 → XP_047282191.1  VWFA and cache domain-containing protein 1 isoform X2

      Related
      ENST00000470527.1

    3. XM_011541862.2 → XP_011540164.1  VWFA and cache domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A3B3ISH2
      Related
      ENSP00000497279.1, ENST00000650260.1
      Conserved Domains (3) summary
      pfam02743
      Location:342 → 409
      Cache_1; Cache domain
      pfam08399
      Location:25 → 90
      VWA_N; VWA N-terminal
      cl00057
      Location:99 → 294
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      64347926..64571142
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337905.1 → XP_054193880.1  VWFA and cache domain-containing protein 1 isoform X1

    2. XM_054337906.1 → XP_054193881.1  VWFA and cache domain-containing protein 1 isoform X2

    3. XM_054337904.1 → XP_054193879.1  VWFA and cache domain-containing protein 1 isoform X4

    4. XM_054337907.1 → XP_054193882.1  VWFA and cache domain-containing protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VU97.2 GenPept UniProtKB/Swiss-Prot:Q5VU97

    Gene LinkOut

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

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