U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    CPED1 cadherin like and PC-esterase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 79974, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    CPED1provided by HGNC
    Official Full Name
    cadherin like and PC-esterase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:26159
    See related
    Ensembl:ENSG00000106034 MIM:620637; AllianceGenome:HGNC:26159
    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
    C7orf58
    Summary
    Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in fat (RPKM 27.4), ovary (RPKM 24.4) and 19 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See CPED1 in Genome Data Viewer
    Location:
    7q31.31
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (120988711..121297442)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (122304057..122612831)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (120628765..120937496)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26556 Neighboring gene RNA, 5S ribosomal pseudogene 240 Neighboring gene inhibitor of growth family member 3 Neighboring gene Sharpr-MPRA regulatory region 12289 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 18 Neighboring gene RNA, 5S ribosomal pseudogene 241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26557 Neighboring gene uncharacterized LOC124901735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26560 Neighboring gene RNA, U6 small nuclear 517, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr7:120931342-120931494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26561 Neighboring gene Wnt family member 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26562 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:121025354-121025551 Neighboring gene hESC enhancers GRCh37_chr7:121035399-121035984 and GRCh37_chr7:121035985-121036569 Neighboring gene FAM3 metabolism regulating signaling molecule C

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A complex chromosome 7q rearrangement identified in a patient with mental retardation, anxiety disorder, and autistic features. Dauwerse JG, et al. Am J Med Genet A, 2010 Feb. PMID 20082467
    2. Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus. Medina-Gomez C, et al. PLoS Genet, 2012 Jul. PMID 22792070, Free PMC Article
    3. Association of regions on chromosomes 6 and 7 with blood pressure in Nigerian families. Tayo BO, et al. Circ Cardiovasc Genet, 2009 Feb. PMID 20031566, Free PMC Article
    4. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. Kemp JP, et al. PLoS Genet, 2014 Jun. PMID 24945404, Free PMC Article
    5. Novel eukaryotic enzymes modifying cell-surface biopolymers. Anantharaman V, et al. Biol Direct, 2010 Jan 7. PMID 20056006, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Variants at the CPED1 locus were strongly associated with bone mineral density at the skull and upper limb sites, but not with lower limb-bone mineral density.
      Title: Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    2. 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.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of regions on chromosomes 6 and 7 with blood pressure in Nigerian families.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    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 meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus.
    EBI GWAS Catalog
    Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ21986, FLJ26813

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    cadherin-like and PC-esterase domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001105533.1 → NP_001099003.1  cadherin-like and PC-esterase domain-containing protein 1 isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' and 3' UTRs, and has multiple differences in the presence and absence of exons at its 3' end, compared to variant 1. The resulting isoform (2) is shorter and contains a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK025639, AY358220, BC017764, BC018685, BQ082412
      Consensus CDS
      CCDS47690.1
      UniProtKB/Swiss-Prot
      A4D0V7
      UniProtKB/TrEMBL
      Q9H6Q5
      Related
      ENSP00000406122.2, ENST00000450913.6
      Conserved Domains (1) summary
      pfam12733
      Location:586 → 667
      Cadherin-like; Cadherin-like beta sandwich domain

    2. NM_024913.5 → NP_079189.4  cadherin-like and PC-esterase domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_079189.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK130323, AL832619, AL832638, BI496654, BQ082412
      Consensus CDS
      CCDS34739.1
      UniProtKB/Swiss-Prot
      A4D0V7, A8K1R3, Q6UXT1, Q86T76, Q86T84, Q8N2T5, Q96NC9
      Related
      ENSP00000309772.5, ENST00000310396.10
      Conserved Domains (2) summary
      pfam12733
      Location:586 → 667
      Cadherin-like; Cadherin-like beta sandwich domain
      pfam13839
      Location:761 → 1020
      PC-Esterase; GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      120988711..121297442
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420856.1 → XP_047276812.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X2

    2. XM_047420857.1 → XP_047276813.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X3

    3. XM_024446941.2 → XP_024302709.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      pfam12733
      Location:412 → 496
      Cadherin-like; Cadherin-like beta sandwich domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      122304057..122612831
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359054.1 → XP_054215029.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X2

    2. XM_054359055.1 → XP_054215030.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X3

    3. XM_054359053.1 → XP_054215028.1  cadherin-like and PC-esterase domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A4D0V7.1 GenPept UniProtKB/Swiss-Prot:A4D0V7

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools