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Aliases for ALMS1 Gene

Aliases for ALMS1 Gene

  • ALMS1, Centrosome And Basal Body Associated Protein 2 3 5
  • Alstrom Syndrome Protein 1 2 3
  • Alstrom Syndrome 1 2 3
  • KIAA0328 4
  • ALSS 3

External Ids for ALMS1 Gene

Previous GeneCards Identifiers for ALMS1 Gene

  • GC02P073622
  • GC02P073823
  • GC02P073587
  • GC02P073524
  • GC02P073466
  • GC02P073612
  • GC02P073348

Summaries for ALMS1 Gene

Entrez Gene Summary for ALMS1 Gene

  • 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]

GeneCards Summary for ALMS1 Gene

ALMS1 (ALMS1, Centrosome And Basal Body Associated Protein) is a Protein Coding gene. Diseases associated with ALMS1 include Alstrom Syndrome and Acanthosis Nigricans. Among its related pathways are Regulation of PLK1 Activity at G2/M Transition and Organelle biogenesis and maintenance. An important paralog of this gene is C10orf90.

UniProtKB/Swiss-Prot for ALMS1 Gene

  • 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALMS1 Gene

Genomics for ALMS1 Gene

Regulatory Elements for ALMS1 Gene

Enhancers for ALMS1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F073417 0.4 ENCODE 11.5 +32.8 32845 1.4 ALMS1 NAT8 SMYD5 GNG5P4 ALMS1-IT1
GH02F073425 0.5 ENCODE 10.9 +40.6 40578 2.0 MYNN ATF2 ALMS1P1 ALMS1 GNG5P4 ALMS1-IT1
GH02F073515 0.4 ENCODE 10.3 +130.5 130540 1.6 JUNB ALMS1P1 ALMS1 TPRKB ALMS1-IT1 GC02P073585
GH02F073892 1.3 FANTOM5 Ensembl ENCODE 4.5 +508.0 507992 3.2 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766 ZNF143 STAMBP SEMA4F SMYD5 ACTG2 C2orf81 MTHFD2 DGUOK TET3 DCTN1 BOLA3
GH02F073384 1 FANTOM5 ENCODE 3.5 +0.3 318 2.3 HDGF MLX ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 ZNF263 SP3 DUSP11 ENSG00000273245 ALMS1P1 DGUOK-AS1 SMYD5 FBXO41 ALMS1 GNG5P4
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ALMS1 on UCSC Golden Path with GeneCards custom track

Promoters for ALMS1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000014007 442 2401 HDGF MLX ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 ZNF263 SP3

Genomic Location for ALMS1 Gene

Chromosome:
2
Start:
73,385,758 bp from pter
End:
73,610,793 bp from pter
Size:
225,036 bases
Orientation:
Plus strand

Genomic View for ALMS1 Gene

Genes around ALMS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALMS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALMS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALMS1 Gene

Proteins for ALMS1 Gene

  • Protein details for ALMS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TCU4-ALMS1_HUMAN
    Recommended name:
    Alstrom syndrome protein 1
    Protein Accession:
    Q8TCU4
    Secondary Accessions:
    • Q53S05
    • Q580Q8
    • Q86VP9
    • Q9Y4G4

    Protein attributes for ALMS1 Gene

    Size:
    4167 amino acids
    Molecular mass:
    460965 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ALMS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ALMS1 Gene

Post-translational modifications for ALMS1 Gene

  • Ubiquitination at Lys 2274, Lys 2333, Lys 2496, Lys 2517, Lys 2624, Lys 2648, Lys 2867, Lys 3057, and Lys 3603
  • Modification sites at PhosphoSitePlus

Other Protein References for ALMS1 Gene

No data available for DME Specific Peptides for ALMS1 Gene

Domains & Families for ALMS1 Gene

Protein Domains for ALMS1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ALMS1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ALMS1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for ALMS1 Gene

Function for ALMS1 Gene

Molecular function for ALMS1 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for ALMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 23414517
GO:0051393 alpha-actinin binding IEA,IBA --
genes like me logo Genes that share ontologies with ALMS1: view
genes like me logo Genes that share phenotypes with ALMS1: view

Human Phenotype Ontology for ALMS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for ALMS1 Gene

Localization for ALMS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALMS1 Gene

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
Jensen Localization Image for ALMS1 Gene COMPARTMENTS Subcellular localization image for ALMS1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 5
endosome 1

Gene Ontology (GO) - Cellular Components for ALMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000922 spindle pole IEA --
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IDA --
GO:0005813 centrosome IDA 15855349
GO:0005814 colocalizes_with centriole IEA,IDA 20844083
genes like me logo Genes that share ontologies with ALMS1: view

Pathways & Interactions for ALMS1 Gene

genes like me logo Genes that share pathways with ALMS1: view

Interacting Proteins for ALMS1 Gene

Gene Ontology (GO) - Biological Process for ALMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle TAS --
GO:0006629 lipid metabolic process IEA --
GO:0007286 spermatid development IEA --
GO:0007605 sensory perception of sound IEA --
GO:0016197 endosomal transport IEA,IMP 22693585
genes like me logo Genes that share ontologies with ALMS1: view

No data available for SIGNOR curated interactions for ALMS1 Gene

Transcripts for ALMS1 Gene

Unigene Clusters for ALMS1 Gene

Alstrom syndrome 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALMS1 Gene

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:
SP6:
SP7: -
SP8:

ExUns: 19b · 19c ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28
SP1: - - - -
SP2: - - -
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:

Relevant External Links for ALMS1 Gene

GeneLoc Exon Structure for
ALMS1
ECgene alternative splicing isoforms for
ALMS1

Expression for ALMS1 Gene

mRNA expression in normal human tissues for ALMS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ALMS1 Gene

This gene is overexpressed in Testis (x4.9).

Protein differential expression in normal tissues from HIPED for ALMS1 Gene

This gene is overexpressed in Liver (25.8), Heart (25.3), and Pancreatic juice (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ALMS1 Gene



Protein tissue co-expression partners for ALMS1 Gene

NURSA nuclear receptor signaling pathways regulating expression of ALMS1 Gene:

ALMS1

SOURCE GeneReport for Unigene cluster for ALMS1 Gene:

Hs.184720

mRNA Expression by UniProt/SwissProt for ALMS1 Gene:

Q8TCU4-ALMS1_HUMAN
Tissue specificity: Expressed in all tissues tested including adipose and pancreas. Expressed by beta-cells of the islets in the pancreas (at protein level).
genes like me logo Genes that share expression patterns with ALMS1: view

Primer Products

Orthologs for ALMS1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALMS1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALMS1 34 35
  • 98.52 (n)
cow
(Bos Taurus)
Mammalia ALMS1 34 35
  • 80.76 (n)
dog
(Canis familiaris)
Mammalia ALMS1 34 35
  • 79.95 (n)
mouse
(Mus musculus)
Mammalia Alms1 34 16 35
  • 74.8 (n)
rat
(Rattus norvegicus)
Mammalia Alms1 34
  • 73.36 (n)
oppossum
(Monodelphis domestica)
Mammalia ALMS1 35
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ALMS1 35
  • 13 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALMS1 35
  • 22 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ALMS1 35
  • 32 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20375 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.3778 34
zebrafish
(Danio rerio)
Actinopterygii ALMS1 35
  • 19 (a)
OneToOne
Species where no ortholog for ALMS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ALMS1 Gene

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

Paralogs for ALMS1 Gene

Paralogs for ALMS1 Gene

(1) SIMAP similar genes for ALMS1 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for ALMS1 Gene

genes like me logo Genes that share paralogs with ALMS1: view

Variants for ALMS1 Gene

Sequence variations from dbSNP and Humsavar for ALMS1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs193919338 Pathogenic 73,490,339(+) GAAGG(C/T)AAAGC reference, stop-gained
rs193919339 Pathogenic 73,572,866(+) GAATG(A/G)AGTGG reference, stop-gained
rs193919340 Pathogenic 73,490,120(+) CTCAC(C/T)GACAT reference, stop-gained
rs387906312 Pathogenic 73,572,649(+) GCAAA(-/C)AACTC reference, frameshift-variant
rs387906313 Pathogenic 73,448,665(+) ACTCT(-/CT)ACTCC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for ALMS1 Gene

Variant ID Type Subtype PubMed ID
dgv635n67 CNV loss 20364138
esv2577218 CNV deletion 19546169
esv2662054 CNV deletion 23128226
esv2759060 CNV gain 17122850
esv3303156 CNV mobile element insertion 20981092
esv3361829 CNV insertion 20981092
esv3591258 CNV loss 21293372
esv3591260 CNV loss 21293372
esv3591261 CNV loss 21293372
esv3591263 CNV loss 21293372
nsv2778 CNV deletion 18451855
nsv2779 CNV insertion 18451855
nsv475751 CNV novel sequence insertion 20440878
nsv477196 CNV novel sequence insertion 20440878
nsv829456 CNV loss 20364138

Variation tolerance for ALMS1 Gene

Residual Variation Intolerance Score: 41% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 25.06; 99.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ALMS1 Gene

Human Gene Mutation Database (HGMD)
ALMS1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALMS1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALMS1 Gene

Disorders for ALMS1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for ALMS1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
alstrom syndrome
  • alström syndrome
acanthosis nigricans
  • an - acanthosis nigricans
giant axonal neuropathy
  • gan
dilated cardiomyopathy
  • congestive cardiomyopathy
cone-rod dystrophy
  • cone-rod dystrophy 5
- elite association - COSMIC cancer census association via MalaCards
Search ALMS1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ALMS1_HUMAN
  • 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. {ECO:0000269 PubMed:11941369, ECO:0000269 PubMed:11941370}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for ALMS1

Genetic Association Database (GAD)
ALMS1
Human Genome Epidemiology (HuGE) Navigator
ALMS1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ALMS1
genes like me logo Genes that share disorders with ALMS1: view

No data available for Genatlas for ALMS1 Gene

Publications for ALMS1 Gene

  1. Spectrum of ALMS1 variants and evaluation of genotype-phenotype correlations in AlstrAPm syndrome. (PMID: 17594715) Marshall J.D. … Naggert J.K. (Hum. Mutat. 2007) 3 22 46 64
  2. Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alstrom syndrome. (PMID: 11941369) Collin G.B. … Naggert J.K. (Nat. Genet. 2002) 3 4 22 64
  3. Mutation of ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alstrom syndrome. (PMID: 11941370) Hearn T. … Wilson D.I. (Nat. Genet. 2002) 3 4 22 64
  4. Human metabolic individuality in biomedical and pharmaceutical research. (PMID: 21886157) Suhre K. … Gieger C. (Nature 2011) 3 46 64
  5. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij J.C. … Florijn R.J. (Ophthalmology 2011) 3 46 64

Products for ALMS1 Gene

Sources for ALMS1 Gene

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