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

    Gene ID: 7840, updated on 28-Oct-2024

    Summary

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    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; AllianceGenome:HGNC:428
    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]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Broad expression in testis (RPKM 15.5), ovary (RPKM 5.0) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ALMS1 in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (73385758..73609919)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (73398811..73623015)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (73612886..73837046)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374803 Neighboring gene Sharpr-MPRA regulatory region 5299 Neighboring gene uncharacterized LOC105374804 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:73612723-73613472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16029 Neighboring gene ribosomal protein SA pseudogene 28 Neighboring gene G protein subunit gamma 5 pseudogene 4 Neighboring gene ALMS1 intronic transcript 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73713947-73714466 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:73737287-73738109 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:73828496-73829695 Neighboring gene ALMS1 pseudogene 1 Neighboring gene N-acetyltransferase 8 (putative)

    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. Alström syndrome is associated with short stature and reduced GH reserve. Romano S, et al. Clin Endocrinol (Oxf), 2013 Oct. PMID 23445176, Free PMC Article
    2. Alström Syndrome. Adam MP, et al. , 1993. PMID 20301444
    3. Prevalent ALMS1 Pathogenic Variants in Spanish Alström Patients. Bea-Mascato B, et al. Genes (Basel), 2021 Feb 16. PMID 33669459, Free PMC Article
    4. [Analysis of ALMS1 gene variants in seven patients with Alström syndrome]. Ding Y, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2021 Feb 10. PMID 33565060
    5. Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alström syndrome. Dassie F, et al. Am J Med Genet A, 2021 Mar. PMID 33410256

    See all (144) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircALMS1 Alleviates Pulmonary Microvascular Endothelial Cell Dysfunction in Pulmonary Hypertension.
      Title: CircALMS1 Alleviates Pulmonary Microvascular Endothelial Cell Dysfunction in Pulmonary Hypertension.
    2. New variants of ALMS1 gene and familial Alstrom syndrome case series.
      Title: New variants of ALMS1 gene and familial Alström syndrome case series.
    3. Overburden of rare ALMS1 deleterious variants in Chinese early-onset type 2 diabetes with severe insulin resistance.
      Title: Overburden of rare ALMS1 deleterious variants in Chinese early-onset type 2 diabetes with severe insulin resistance.
    4. Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.
      Title: Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.
    5. Unraveling Alstrom syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family.
      Title: Unraveling Alström syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family.
    6. Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes.
      Title: Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes.
    7. Identification of ALMS1 pathogenic variants in Chinese patients with Alstrom syndrome.
      Title: Identification of ALMS1 pathogenic variants in Chinese patients with Alström syndrome.
    8. Whole-Genome Sequencing Identifies Novel Heterozygous Mutation in ALMS1 in Three Men With Both Peyronie's and Dupuytren's Disease.
      Title: Whole-Genome Sequencing Identifies Novel Heterozygous Mutation in ALMS1 in Three Men With Both Peyronie's and Dupuytren's Disease.
    9. New pathogenic variants of ALMS1 gene in two Chinese families with Alstrom Syndrome.
      Title: New pathogenic variants of ALMS1 gene in two Chinese families with Alström Syndrome.
    10. Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alstrom syndrome.
      Title: Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alström syndrome.
    Submit: New GeneRIF Correction See all GeneRIFs (60)

    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

    Associated conditions

    Description Tests
    Alstrom syndrome
    MedGen: C0268425 OMIM: 203800 GeneReviews: Alstrom Syndrome
    		not available

    EBI GWAS Catalog

    Description
    A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
    EBI GWAS Catalog
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genetic loci influencing kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
    EBI GWAS Catalog
    Human metabolic individuality in biomedical and pharmaceutical research.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    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

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    		  
    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
    		  
    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
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in spindle pole IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    centrosome-associated protein ALMS1
    Names
    Alstrom syndrome 1
    Alstrom syndrome 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.

    Genomic

    1. NG_011690.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001378454.1 → NP_001365383.1  centrosome-associated protein ALMS1 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
      Consensus CDS
      CCDS42697.1
      UniProtKB/Swiss-Prot
      A0A087WZY3, Q53S05, Q580Q8, Q86VP9, Q8TCU4, Q9Y4G4
      UniProtKB/TrEMBL
      A0A087WTU9
      Related
      ENSP00000482968.1, ENST00000613296.6
      Conserved Domains (2) summary
      pfam18727
      Location:1770 → 1816
      ALMS_repeat; Alstrom syndrome repeat
      pfam15309
      Location:4032 → 4163
      ALMS_motif; ALMS motif

    2. NM_015120.4 → NP_055935.4  centrosome-associated protein ALMS1 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
      UniProtKB/TrEMBL
      A0A087WTU9
      Related
      ENSP00000478155.1, ENST00000484298.5
      Conserved Domains (2) summary
      pfam06583
      Location:1425 → 1573
      Neogenin_C; Neogenin C-terminus
      pfam15309
      Location:4034 → 4165
      ALMS_motif; ALMS motif

    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_000002.12 Reference GRCh38.p14 Primary Assembly

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

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791766.1 Reference GRCh38.p14 PATCHES

      Range
      55253..279417
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      73398811..73623015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TCU4.4 GenPept UniProtKB/Swiss-Prot:Q8TCU4

    Gene LinkOut

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

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