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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 Cell Cycle, Mitotic 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.

Additional gene information for ALMS1 Gene

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

GeneHancer (GH) Regulatory Elements for ALMS1 Gene

Promoters and enhancers for ALMS1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J073384 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 653.5 +0.3 317 2.3 HDGF SMAD1 MLX ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 E2F8 ALMS1 LOC105374804 ENSG00000273245 DUSP11 ALMS1P1 DGUOK-AS1 DGUOK GNG5P4
GH02J074196 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 40.7 +813.0 812989 3.9 CLOCK FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ENSG00000279070 MTHFD2 PCGF1 ENSG00000273245 INO80B DUSP11 ALMS1 HTRA2 WBP1 AUP1
GH02J073069 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.2 -314.8 -314819 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 SFXN5 DUSP11 CCT7 ENSG00000273245 ALMS1 TPRKB SMYD5 DGUOK-AS1 RAB11FIP5 GC02M073124
GH02J073175 Enhancer 1.6 FANTOM5 Ensembl ENCODE 24.7 -209.1 -209104 3.2 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SLC30A9 ZNF213 E2F8 ALMS1 ENSG00000273245 SMYD5 DUSP11 SFXN5 PRADC1 NOTO SPR EMX1 CCT7
GH02J073109 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.4 -273.9 -273863 5.2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS SP3 SP5 NFYC RAB11FIP5 ENSG00000272702 ENSG00000273245 DUSP11 SFXN5 ALMS1 EMX1 SPR SMYD5 GC02M073122
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ALMS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ALMS1 gene promoter:

Genomic Locations for ALMS1 Gene

Genomic Locations for ALMS1 Gene
chr2:73,385,758-73,610,793
(GRCh38/hg38)
Size:
225,036 bases
Orientation:
Plus strand
chr2:73,612,886-73,837,920
(GRCh37/hg19)

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:
    • A0A087WZY3
    • Q53S05
    • Q580Q8
    • Q86VP9
    • Q9Y4G4

    Protein attributes for ALMS1 Gene

    Size:
    4168 amino acids
    Molecular mass:
    461062 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 Lys3603, posLast=30573057, Lys2867, posLast=26482648, posLast=26242624, Lys2517, Lys2496, posLast=23332333, and posLast=22742274
  • 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

Gene Families for ALMS1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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 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.

Phenotypes From GWAS Catalog for ALMS1 Gene

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 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

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

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 IDA 20844083
GO:0005829 cytosol IDA,TAS --
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:0010389 regulation of G2/M transition of mitotic cell cycle TAS --
GO:0016197 endosomal transport IMP,IEA 22693585
GO:0051492 regulation of stress fiber assembly IMP,IEA 22693585
GO:0097711 ciliary basal body-plasma membrane docking TAS --
genes like me logo Genes that share ontologies with ALMS1: view

No data available for SIGNOR curated interactions for ALMS1 Gene

Drugs & Compounds for ALMS1 Gene

No Compound Related Data Available

Transcripts for ALMS1 Gene

mRNA/cDNA for ALMS1 Gene

Unigene Clusters for ALMS1 Gene

Alstrom syndrome 1:
Representative Sequences:

Clone 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 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
Regions:
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

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 33
  • 98.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ALMS1 34 33
  • 80.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ALMS1 34 33
  • 79.95 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Alms1 16 34 33
  • 74.8 (n)
rat
(Rattus norvegicus)
Mammalia Alms1 33
  • 73.36 (n)
oppossum
(Monodelphis domestica)
Mammalia ALMS1 34
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ALMS1 34
  • 13 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALMS1 34
  • 22 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ALMS1 34
  • 32 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20375 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.3778 33
zebrafish
(Danio rerio)
Actinopterygii ALMS1 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for ALMS1: view image

Paralogs for ALMS1 Gene

Paralogs for ALMS1 Gene

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

  • ALMS1_HUMAN
  • A1YZ18_HUMAN
  • A6NMY3_HUMAN
  • B8ZZJ3_HUMAN
  • D6W5H5_HUMAN
  • H7C1D9_HUMAN

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 Variation AA Info Type
rs1007457582 uncertain-significance, Alstrom syndrome 73,453,929(+) A/G coding_sequence_variant, missense_variant
rs10199680 benign, not specified, Alstrom syndrome 73,534,815(+) C/T intron_variant
rs1034630858 pathogenic, Alstrom syndrome 73,453,093(+) ACTCAC/AC coding_sequence_variant, frameshift
rs1043429291 uncertain-significance, Alstrom syndrome 73,490,879(+) C/T coding_sequence_variant, missense_variant
rs1047348249 uncertain-significance, Alstrom syndrome 73,452,547(+) A/G coding_sequence_variant, missense_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)

Additional Variant Information for ALMS1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for ALMS1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for ALMS1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
alstrom syndrome
  • alms
acanthosis nigricans
  • an - acanthosis nigricans
bardet-biedl syndrome 16
  • bbs16
bardet-biedl syndrome 2
  • bbs2
giant axonal neuropathy
  • gan1
- 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.

Additional Disease Information for ALMS1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 Alström syndrome. (PMID: 17594715) Marshall JD … Naggert JK (Human mutation 2007) 3 22 44 58
  2. Mutation of ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alström syndrome. (PMID: 11941370) Hearn T … Wilson DI (Nature genetics 2002) 3 4 22 58
  3. Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alström syndrome. (PMID: 11941369) Collin GB … Naggert JK (Nature genetics 2002) 3 4 22 58
  4. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. (PMID: 21931564) Nicholson G … Holmes CC (PLoS genetics 2011) 3 44 58
  5. Human metabolic individuality in biomedical and pharmaceutical research. (PMID: 21886157) Suhre K … Gieger C (Nature 2011) 3 44 58

Products for ALMS1 Gene

Sources for ALMS1 Gene

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