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ALMS1 Gene

protein-coding   GIFtS: 62
GCID: GC02P073612

Alstrom Syndrome 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Alstrom Syndrome 11 2
ALSS2 5
KIAA03283 5
Alstrom Syndrome Protein 12

External Ids:    HGNC: 4281   Entrez Gene: 78402   Ensembl: ENSG000001161277   OMIM: 6068445   UniProtKB: Q8TCU43   

Export aliases for ALMS1 gene to outside databases

Previous GC identifers: GC02P073622 GC02P073823 GC02P073587 GC02P073524 GC02P073466 GC02P073348


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ALMS1 Gene:
This gene encodes a protein containing a large tandem-repeat domain. The mouse ortholog of this gene has been
shown to function in ciliogenesis in inner medullary collecting duct cells. Mutations in this gene have been
associated with Alstrom syndrome. Alternative splice variants have been described but their full length sequences
have not been determined.(provided by RefSeq, Mar 2009)

GeneCards Summary for ALMS1 Gene:
ALMS1 (Alstrom syndrome 1) is a protein-coding gene. Diseases associated with ALMS1 include alstrom syndrome, and acanthosis nigricans. An important paralog of this gene is C10orf90.

UniProtKB/Swiss-Prot: ALMS1_HUMAN, Q8TCU4
Function: Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the
localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of
primary cilia (PC), microtubule-based structures that protrude from the surface of epithelial cells




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000002.12  NC_018913.2  NT_022184.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the ALMS1 gene promoter:
         TBP   Pax-5   AML1a   Egr-1   FOXD1   STAT5A   TFIID   Sox9   ZID   Zic3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidALMS1 promoter sequence
   Search Chromatin IP Primers for ALMS1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ALMS1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p13   Ensembl cytogenetic band:  2p13.1   HGNC cytogenetic band: 2p13.1

ALMS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALMS1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P073612:  view genomic region     (about GC identifiers)

Start:
73,612,886 bp from pter      End:
73,837,920 bp from pter
Size:
225,035 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: ALMS1_HUMAN, Q8TCU4 (See protein sequence)
Recommended Name: Alstrom syndrome protein 1  
Size: 4167 amino acids; 460965 Da
Developmental stage: Widely expressed in fetal tissues. Detected in fetal pancreas, skeletal muscle, liver, kidney
and brain (at protein level). Expressed in fetal aorta and brain
Secondary accessions: Q53S05 Q580Q8 Q86VP9 Q9Y4G4
Alternative splicing: 3 isoforms:  Q8TCU4-1   Q8TCU4-2   Q8TCU4-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ALMS1: NX_Q8TCU4

Explore proteomics data for ALMS1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys2274, Lys2333, Lys2496, Lys2517, Lys2624, Lys2648, Lys2867, Lys3057, Lys3603
  • Modification sites at PhosphoSitePlus

  • See ALMS1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055935.4  
    ENSEMBL proteins: 
     ENSP00000386627   ENSP00000264448   ENSP00000399833   ENSP00000366944  
    Reactome Protein details: Q8TCU4

    ALMS1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for ALMS1

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    LSBio Antibodies in human, mouse, rat for ALMS1

    ALMS1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for ALMS1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for ALMS1
    Cloud-Clone Corp. CLIAs for ALMS1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR028781 ALMS1

    Graphical View of Domain Structure for InterPro Entry Q8TCU4

    ProtoNet protein and cluster: Q8TCU4


    ALMS1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ALMS1_HUMAN, Q8TCU4
    Function: Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the
    localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of
    primary cilia (PC), microtubule-based structures that protrude from the surface of epithelial cells

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding IPI--
         
    ALMS1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for ALMS1:
     Synthetic lethal with Ras  Synthetic lethal with c-Myc af 

         12 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Alms1):
     adipose tissue  behavior/neurological  cellular  endocrine/exocrine gland  growth/size/body 
     hearing/vestibular/ear  homeostasis/metabolism  immune system  liver/biliary system  renal/urinary system 
     reproductive system  vision/eye 

    ALMS1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ALMS1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for ALMS1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ALMS1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ALMS1

    miRNA
    Products:
        
    miRTarBase miRNAs that target ALMS1:
    hsa-mir-22-3p (MIRT050457), hsa-mir-197-3p (MIRT004192), hsa-mir-99b-3p (MIRT038525), hsa-mir-375 (MIRT019997), hsa-mir-92a-3p (MIRT049216), hsa-mir-21-5p (MIRT031049)

    Block miRNA regulation of human, mouse, rat ALMS1 using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate ALMS1:
    hsa-miR-3163 hsa-miR-548d-3p hsa-miR-548am hsa-miR-548x
    SwitchGear 3'UTR luciferase reporter plasmidALMS1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ALMS1
    Predesigned siRNA for gene silencing in human, mouse, rat ALMS1

    Gene Editing
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    OriGene clones in human, mouse for ALMS1 (see all 5)
    OriGene ORF clones in mouse, rat for ALMS1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: ALMS1 (NM_015120)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ALMS1
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ALMS1

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for ALMS1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALMS1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ALMS1_HUMAN, Q8TCU4: Cytoplasm. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cytoplasm,
    cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, spindle pole. Note=Associated with centrosomes and
    basal bodies at the base of primary cilia. Specifically locates to the proximal ends of centrioles and basal
    bodies. Colocalizes partially with NCAPD2 at these sites. During mitosis localizes to both spindle poles
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    cytosol4
    nucleus3

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000922spindle pole IEA--
    GO:0005737cytoplasm IDA--
    GO:0005813centrosome IDA15855349
    GO:0005814colocalizes with centriole IDA--
    GO:0005829cytosol TAS--

    ALMS1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for ALMS1 About    
    See pathways by source

    SuperPathContained pathways About
    1Regulation of PLK1 Activity at G2/M Transition
    Recruitment of mitotic centrosome proteins and complexes0.86
    Regulation of PLK1 Activity at G2/M Transition0.77
    Loss of Nlp from mitotic centrosomes0.86
    G2/M Transition0.70
    Centrosome maturation0.86
    Mitotic G2-G2/M phases0.69
    Loss of proteins required for interphase microtubule organizationfrom the centrosome0.86
    2Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    Cell Cycle0.90

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    4 Reactome Pathways for ALMS1
        Recruitment of mitotic centrosome proteins and complexes
    Loss of proteins required for interphase microtubule organization,from the centrosome
    Regulation of PLK1 Activity at G2/M Transition
    Loss of Nlp from mitotic centrosomes



    ALMS1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including ALMS1: 
              Primary Cilia in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for ALMS1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for ALMS1 (Q8TCU41, 3 ENSP000002644484) via UniProtKB, MINT, STRING, and/or I2D (see all 57)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MEGF10Q96KG73, ENSP000002744734I2D: score=2 STRING: ENSP00000274473
    DYSFO759231EBI-308651,EBI-2799016
    CEP135ENSP000002572874STRING: ENSP00000257287
    CEP152ENSP000003822714STRING: ENSP00000382271
    CEP164ENSP000002789354STRING: ENSP00000278935
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000086G2/M transition of mitotic cell cycle TAS--
    GO:0000278mitotic cell cycle TAS--
    GO:0008150biological_process ----
    GO:0016197endosomal transport IMP--
    GO:0051492regulation of stress fiber assembly IMP--

    ALMS1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ALMS1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for ALMS1 gene: 
    NM_015120.4  

    Unigene Cluster for ALMS1:

    Alstrom syndrome 1
    Hs.184720  [show with all ESTs]
    Unigene Representative Sequence: AJ417593
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409009(uc002sjg.3 uc002sjh.1) ENST00000264448(uc002sje.1 uc002sjf.1)
    ENST00000423048(uc010fev.1) ENST00000484298 ENST00000476650 ENST00000464408
    ENST00000490821 ENST00000377715
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat ALMS1 using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate ALMS1:
    hsa-miR-3163 hsa-miR-548d-3p hsa-miR-548am hsa-miR-548x
    SwitchGear 3'UTR luciferase reporter plasmidALMS1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ALMS1
    Predesigned siRNA for gene silencing in human, mouse, rat ALMS1
    Clone
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    OriGene clones in human, mouse for ALMS1 (see all 5)
    OriGene ORF clones in mouse, rat for ALMS1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: ALMS1 (NM_015120)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ALMS1
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ALMS1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for ALMS1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ALMS1
      QuantiTect SYBR Green Assays in human, mouse, rat ALMS1
      QuantiFast Probe-based Assays in human, mouse, rat ALMS1

    Additional mRNA sequence: 

    AB002326.3 AJ417593.2 AL833495.1 BC035025.2 BC050330.1 BX647706.1 BX648632.1 EF151141.1 

    13 DOTS entries:

    DT.314966  DT.75155839  DT.100816254  DT.92422157  DT.100036543  DT.100671819  DT.99997664  DT.100036545 
    DT.101963353  DT.121008213  DT.121008226  DT.92422155  DT.95299663 

    Selected AceView cDNA sequences (see all 146):

    BU154288 BU617556 AA913775 AB002326 BM875692 AL832273 R14339 AA749051 
    AW082244 F12602 AL041387 AW386108 BM452035 BU727724 AX751581 BX951838 
    AJ417593 NM_015120 BM723326 AI741793 BX088771 F10219 BE891274 AL045603 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for ALMS1 (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a ·
    SP1:                                                                          -     -     -     -     -                                                         
    SP2:                                                                          -     -     -     -     -                                                         
    SP3:                                                                          -     -     -     -     -                 -                                       
    SP4:                                                                          -     -     -     -     -                                                         
    SP5:                                                                                                                                                            

    ExUns: 19b · 19c ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28
    SP1:        -     -     -                                   -               
    SP2:        -     -     -                                                   
    SP3:                                                                        
    SP4:                                                                        
    SP5:        -                                                               


    ECgene alternative splicing isoforms for ALMS1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ALMS1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTATTTTAG
    ALMS1 Expression
    About this image


    ALMS1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Thymus (Hematopoietic System)
             Double Positive Thymocytes Thymus
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
     
     Blood (Cardiovascular System)
             Double Positive Thymocytes Thymus
    ALMS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ALMS1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.184720

    UniProtKB/Swiss-Prot: ALMS1_HUMAN, Q8TCU4
    Tissue specificity: Expressed in all tissues tested including adipose and pancreas. Expressed by beta-cells of the
    islets in the pancreas (at protein level)

        Pathway & Disease-focused RT2 Profiler PCR Array including ALMS1: 
              Primary Cilia in human mouse rat

    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for ALMS1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ALMS1
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    QuantiFast Probe-based Assays in human, mouse, rat ALMS1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALMS1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for ALMS1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Alms11 , 5 Alstrom syndrome 1 homolog (human)5
    Alstrom syndrome 11
    74.8(n)1
    60.7(a)1
      6 (37.48 cM)5
    2362661  NM_145223.21  NP_660258.21 
     855875315 
    chicken
    (Gallus gallus)
    Aves ALMS16
    Alstrom syndrome 1
    22(a)
    1 ↔ 1
    4(89120583-89171978)
    lizard
    (Anolis carolinensis)
    Reptilia ALMS16
    Alstrom syndrome 1
    32(a)
    1 ↔ 1
    GL343639.1(35404-137651)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.37782 Xenopus laevis transcribed sequences 75.56(n)    48031315 
    zebrafish
    (Danio rerio)
    Actinopterygii ALMS16
    Alstrom syndrome 1
    19(a)
    1 ↔ 1
    13(8733976-8771516) ENSDARG00000074779


    ENSEMBL Gene Tree for ALMS1 (if available)
    TreeFam Gene Tree for ALMS1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ALMS1 gene
    C10orf902  
    1 SIMAP similar gene for ALMS1 using alignment to 6 protein entries:     ALMS1_HUMAN (see all proteins):
    ALMS1P

    ALMS1 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for ALMS1
    PGOHUM00000240684 PGOHUM00000240685


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for ALMS1 (see all 4799)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1939226931,2
    Cprobable-pathogenic173411032(+) TTCCTA/GCTCAC 2 Y C mis10--------
    rs1441780641,2
    --73346427(+) ATGGGA/CTGTCC 1 -- us2k10--------
    rs744401231,2
    F--73346588(+) GCTTTT/ATCAGA 1 -- us2k11Minor allele frequency- A:0.07WA 118
    rs75768241,2
    C,F,A,H--73346772(+) ctgttA/Gttaac 1 -- us2k128Minor allele frequency- G:0.32NS EA NA WA CSA 2776
    rs1863434191,2
    --73346866(+) TTAGAC/TGGAAG 1 -- us2k10--------
    rs1164049041,2
    F--73347177(+) AACTCC/TAAGAC 1 -- us2k11Minor allele frequency- T:0.01NA 120
    rs1507537761,2
    --73347461(+) ATTGGA/GGGTAC 1 -- us2k10--------
    rs1907422371,2
    --73347537(+) TGAAGC/TGGTCA 1 -- us2k10--------
    rs124658671,2
    C,F,H--73347593(+) CAAAAC/TATATG 1 -- us2k124Minor allele frequency- T:0.42NS EA NA WA CSA 2352
    rs1828992211,2
    --73347638(+) TAACAG/TCTGGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ALMS1 (73612886 - 73837920 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for ALMS1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2577218CNV Deletion19546169
    esv2662054CNV Deletion23128226
    esv267436CNV Insertion20981092
    nsv2779CNV Insertion18451855
    nsv829456CNV Loss20364138
    dgv635n67CNV Loss20364138
    nsv874267CNV Loss21882294
    nsv2778CNV Loss18451855
    essv105CNV CNV17122850
    dgv1197e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): ALMS1
    Locus Specific Mutation Databases (LSDB): ALMS1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ALMS1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606844   
    OMIM disorders: 203800  
    UniProtKB/Swiss-Prot: ALMS1_HUMAN, Q8TCU4
  • Alstrom syndrome (ALMS) [MIM:203800]: A rare autosomal recessive disorder characterized by progressive
    cone-rod retinal dystrophy, neurosensory hearing loss, early childhood obesity and diabetes mellitus type 2.
    Dilated cardiomyopathy, acanthosis nigricans, male hypogonadism, hypothyroidism, developmental delay and hepatic
    dysfunction can also be associated with the syndrome. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 20 diseases for ALMS1:    
    About MalaCards
    alstrom syndrome    acanthosis nigricans    cellulitis    cone-rod dystrophy
    bardet-biedl syndrome    retinal disease    leber congenital amaurosis    sensorineural hearing loss
    hypogonadism    hypothyroidism    dilated cardiomyopathy    retinitis
    kidney disease    blindness    insulin resistance    diabetes mellitus
    obesity    hepatitis    multiple myeloma    myeloma

    4 diseases from the University of Copenhagen DISEASES database for ALMS1:
    Bardet-Biedl syndrome     Sensorineural hearing loss     Blindness     Dilated cardiomyopathy

    ALMS1 for disorders           About GeneDecksing

    GeneTests: ALMS1
    GeneReviews: ALMS1
    Genetic Association Database (GAD): ALMS1
    Human Genome Epidemiology (HuGE) Navigator: ALMS1 (9 documents)

    Export disorders for ALMS1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ALMS1 gene, integrated from 10 sources (see all 59):
    (articles sorted by number of sources associating them with ALMS1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutation of ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alstrom syndrome. (PubMed id 11941370)1, 2, 9 Hearn T.... Wilson D.I. (Nat. Genet. 2002)
    2. Spectrum of ALMS1 variants and evaluation of genotype-phenotype correlations in AlstrAPm syndrome. (PubMed id 17594715)1, 4, 9 Marshall J.D....Naggert J.K. (Hum. Mutat. 2007)
    3. Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alstrom syndrome. (PubMed id 11941369)1, 2, 9 Collin G.B....Naggert J.K. (Nat. Genet. 2002)
    4. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. (PubMed id 21931564)1, 4 Nicholson G....Holmes C.C. (PLoS Genet. 2011)
    5. Human metabolic individuality in biomedical and pharmaceutical research. (PubMed id 21886157)1, 4 Suhre K....Gieger C. (Nature 2011)
    6. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PubMed id 20801516)1, 4 Booij J.C....Florijn R.J. (Ophthalmology 2011)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    8. New loci associated with kidney function and chronic kidney disease. (PubMed id 20383146)1, 4 KAPttgen A....Fox C.S. (Nat. Genet. 2010)
    9. Centriolar association of ALMS1 and likely centrosomal functions of the ALMS motif-containing proteins C10orf90 and KIAA1731. (PubMed id 20844083)1, 2 Knorz V.J.... Hearn T. (Mol. Biol. Cell 2010)
    10. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7840 HGNC: 428 AceView: ALMS1 Ensembl:ENSG00000116127 euGenes: HUgn7840
    ECgene: ALMS1 H-InvDB: ALMS1

    (According to HUGE)
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    HUGE: KIAA0328

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ALMS1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=ALMS1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ALMS1 gene:
    Search GeneIP for patents involving ALMS1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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