Free for academic non-profit institutions. Other users need a Commercial license

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 Giant Axonal Neuropathy. Among its related pathways are Regulation of PLK1 Activity at G2/M Transition and Organelle biogenesis and maintenance.

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 CIViC summary , 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
GH02G073892 2 FANTOM5 Ensembl ENCODE dbSUPER 4.5 +508.0 507992 3.2 CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 DUSP11 PCGF1 STAMBP SEMA4F ENSG00000273245 SMYD5 ACTG2 MTHFD2 CCDC142 DGUOK
GH02G073384 1.4 FANTOM5 ENCODE 3.5 +0.3 318 2.3 HDGF MLX ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 ZNF207 ZNF263 DUSP11 ALMS1P1 ENSG00000273245 DGUOK-AS1 SMYD5 FBXO41 ALMS1 GNG5P4
GH02G073425 0.4 ENCODE 10.9 +40.6 40578 2.0 MYNN ATF2 ALMS1P1 ALMS1 GNG5P4 ALMS1-IT1
GH02G073515 0.4 ENCODE 10.3 +130.5 130540 1.6 JUNB ALMS1P1 ALMS1 TPRKB ALMS1-IT1 GC02P073585
GH02G073857 1 FANTOM5 2.5 +471.3 471280 0.2 HDAC1 ATF1 CBX3 PKNOX1 TBL1XR1 ARNT CHAMP1 TCF12 ZNF766 GATA2 SLC4A5 ALMS1 LOC105374806 LOC105374807
- Elite enhancer and/or Elite enhancer-gene association 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
ENSR00000119053 242 2001 HDGF MLX ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 ZNF207 ZNF263

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 posLast=22742274, Lys2333, posLast=24962496, posLast=25172517, posLast=26242624, posLast=26482648, posLast=28672867, posLast=30573057, and posLast=36033603
  • 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

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ALMS1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 4
endosome 1

Gene Ontology (GO) - Cellular Components for ALMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000922 spindle pole IEA --
GO:0005813 centrosome IDA 15855349
GO:0005814 colocalizes_with centriole IEA,IDA 20844083
GO:0005829 cytosol TAS,IDA --
GO:0005929 cilium IEA --
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 IMP,IEA 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:

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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).

Evidence on tissue expression from TISSUES for ALMS1 Gene

  • Liver(4.4)
  • Nervous system(4.4)
  • Blood(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ALMS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • hypothalamus
  • inner ear
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • pituitary gland
  • skull
  • thyroid
  • tooth
Thorax:
  • breast
  • bronchus
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • adrenal gland
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • ureter
  • urinary bladder
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
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

(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

No data available for Paralogs for ALMS1 Gene

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
rs367877017 Pathogenic 73,573,081(+) TTCTT(A/C/T)GGATT reference, missense, stop-gained
rs387906312 Pathogenic 73,572,649(+) GCAAA(-/C)AACTC 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

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

Disorder Aliases PubMed IDs
alstrom syndrome
  • alström syndrome
giant axonal neuropathy
  • gan
bardet-biedl syndrome 16
  • bbs16
acanthosis nigricans
  • an - acanthosis nigricans
leber congenital amaurosis
  • lca
- 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

Content
Loading form....