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    ALMS1 ALMS1 centrosome and basal body associated protein [ Homo sapiens (human) ]

    Gene ID: 7840, updated on 8-Jul-2021

    Summary

    Official Symbol
    ALMS1provided by HGNC
    Official Full Name
    ALMS1 centrosome and basal body associated proteinprovided by HGNC
    Primary source
    HGNC:HGNC:428
    See related
    Ensembl:ENSG00000116127 MIM:606844
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALSS
    Summary
    This gene encodes a protein containing a large tandem-repeat domain as well as additional low complexity regions. The encoded protein functions in microtubule organization, particularly in the formation and maintanance of cilia. Mutations in this gene cause Alstrom syndrome. There is a pseudogene for this gene located adjacent in the same region of chromosome 2. Alternative splice variants have been described but their full length nature has not been determined. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in testis (RPKM 15.5), ovary (RPKM 5.0) and 21 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See ALMS1 in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (73385758..73609919)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (73612886..73837046)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5299 Neighboring gene uncharacterized LOC105374804 Neighboring gene ribosomal protein SA pseudogene 28 Neighboring gene G protein subunit gamma 5 pseudogene 4 Neighboring gene ALMS1 intronic transcript 1 Neighboring gene ALMS1 pseudogene 1 Neighboring gene N-acetyltransferase 8 (putative)

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
    GeneReviews: Not available
    Alstrom syndrome
    MedGen: C0268425 OMIM: 203800 GeneReviews: Alstrom Syndrome
    Compare labs
    An atlas of genetic influences on human blood metabolites.
    GeneReviews: Not available
    Genetic loci influencing kidney function and chronic kidney disease.
    GeneReviews: Not available
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    GeneReviews: Not available
    Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
    GeneReviews: Not available
    Human metabolic individuality in biomedical and pharmaceutical research.
    GeneReviews: Not available
    New loci associated with kidney function and chronic kidney disease.
    GeneReviews: Not available

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with Alstrom syndrome 1 (ALMS1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0328, DKFZp686A118, DKFZp686D1828

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables microtubule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of centriole replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within regulation of stress fiber assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    colocalizes_with centriole IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cilium IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in spindle pole IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    Alstrom syndrome protein 1
    Names
    Alstrom syndrome 1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_011690.1 RefSeqGene

      Range
      5001..229167
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_741

    mRNA and Protein(s)

    1. NM_001378454.1NP_001365383.1  Alstrom syndrome protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes isoform 2. This transcript and NM_015120.4 have the same exon combination but differ in the length of the encoded proteins.
      Source sequence(s)
      AC074008, AC092653, AC096546, KF573641
      Related
      ENSP00000482968.1, ENST00000613296.6
      Conserved Domains (2) summary
      pfam18727
      Location:17701816
      ALMS_repeat; Alstrom syndrome repeat
      pfam15309
      Location:40324163
      ALMS_motif; ALMS motif
    2. NM_015120.4NP_055935.4  Alstrom syndrome protein 1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. This transcript and NM_001378454.1 have the same exon combination but differ in the length of the encoded proteins.
      Source sequence(s)
      AC074008, AC092653, AC096546, AJ417593
      Consensus CDS
      CCDS42697.1
      UniProtKB/Swiss-Prot
      Q8TCU4
      Related
      ENSP00000478155.1, ENST00000484298.5
      Conserved Domains (2) summary
      pfam06583
      Location:14251573
      Neogenin_C; Neogenin C-terminus
      pfam15309
      Location:40344165
      ALMS_motif; ALMS motif

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      73385758..73609919
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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