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

Gene ID: 7840, updated on 9-Aug-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
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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
not available
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)

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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_001378454.1NP_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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