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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

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