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    LDLRAD1 low density lipoprotein receptor class A domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 388633, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LDLRAD1provided by HGNC
    Official Full Name
    low density lipoprotein receptor class A domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:32069
    See related
    Ensembl:ENSG00000203985 AllianceGenome:HGNC:32069
    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 be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in lung (RPKM 3.4), stomach (RPKM 0.6) and 5 other tissues See more
    Orthologs
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    Genomic context

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    See LDLRAD1 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (54007298..54018186, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53890196..53901083, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54472971..54483859, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 913 Neighboring gene Sharpr-MPRA regulatory region 3629 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:54422389-54423588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54424449-54425155 Neighboring gene leucine rich repeat containing 42 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 12 Neighboring gene NANOG hESC enhancer GRCh37_chr1:54485757-54486258 Neighboring gene MPRA-validated peak239 silencer Neighboring gene transmembrane protein 59 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 915 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:54518370-54518924 and GRCh37_chr1:54518925-54519480 Neighboring gene transcription elongation factor A N-terminal and central domain containing 2 Neighboring gene microRNA 4781

    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. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Corominas R, et al. Nat Commun, 2014 Apr 11. PMID 24722188, Free PMC Article
    2. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article
    3. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Fragoza R, et al. Nat Commun, 2019 Sep 12. PMID 31515488, Free PMC Article
    4. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (8) 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

    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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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    low-density lipoprotein receptor class A domain-containing protein 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_001010978.4 → NP_001010978.2  low-density lipoprotein receptor class A domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001010978.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC103740, BC127708, BM977091, CF887342
      Consensus CDS
      CCDS30725.1
      UniProtKB/Swiss-Prot
      A0PJY0, B7ZME3, Q5T6Z9, Q5T700
      Related
      ENSP00000360411.1, ENST00000371360.2

    2. NM_001276392.2 → NP_001263321.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001263321.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC103740, BC127709, BM977091, CF887342
      Consensus CDS
      CCDS60147.1
      UniProtKB/Swiss-Prot
      Q5T700
      Related
      ENSP00000411017.1, ENST00000420619.5

    3. NM_001276393.2 → NP_001263322.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001263322.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      BC103740, BC140760, BM977091, CF887342
      Consensus CDS
      CCDS60146.1
      UniProtKB/Swiss-Prot
      Q5T700
      Related
      ENSP00000445871.1, ENST00000545928.5

    4. NM_001276394.2 → NP_001263323.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two in-frame exons in the coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      BC103740, BM977091, CF887342
      Consensus CDS
      CCDS60145.1
      UniProtKB/Swiss-Prot
      Q5T700
      Related
      ENSP00000360413.3, ENST00000371362.7

    5. NM_001276395.2 → NP_001263324.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an exon and uses an alternate splice site in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC103740, BC171743, BM977091, CF887342

    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
      54007298..54018186 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001264.2 → XP_016856753.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform X2

    2. XM_011541446.2 → XP_011539748.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      53890196..53901083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336521.1 → XP_054192496.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform X2

    2. XM_054336520.1 → XP_054192495.1  low-density lipoprotein receptor class A domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T700.1 GenPept UniProtKB/Swiss-Prot:Q5T700

    Gene LinkOut

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

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