ALMS1

gene
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Also known as KIAA0328

Summary

ALMS1 (ALMS1 centrosome and basal body associated protein, HGNC:428) is a protein-coding gene on chromosome 2p13.1, encoding Centrosome-associated protein ALMS1 (Q8TCU4). Involved in PCM1-dependent intracellular transport.

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.

Source: NCBI Gene 7840 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Alstrom syndrome (Definitive, ClinGen)
  • GWAS associations: 75
  • Clinical variants (ClinVar): 7,452 total — 635 pathogenic, 297 likely-pathogenic
  • Phenotypes (HPO): 144
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_001378454

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:428
Approved symbolALMS1
NameALMS1 centrosome and basal body associated protein
Location2p13.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0328
Ensembl geneENSG00000116127
Ensembl biotypeprotein_coding
OMIM606844
Entrez7840

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 9 protein_coding, 7 nonsense_mediated_decay, 6 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000423048, ENST00000464408, ENST00000484298, ENST00000490821, ENST00000613296, ENST00000614410, ENST00000620466, ENST00000651057, ENST00000651434, ENST00000651750, ENST00000652487, ENST00000682565, ENST00000682675, ENST00000682801, ENST00000682859, ENST00000682889, ENST00000683108, ENST00000683147, ENST00000683791, ENST00000684148, ENST00000684197, ENST00000684460, ENST00000684548, ENST00000684590, ENST00000684656

RefSeq mRNA: 2 — MANE Select: NM_001378454 NM_001378454, NM_015120

CCDS: CCDS42697

Canonical transcript exons

ENST00000613296 — 23 exons

ExonStartEnd
ENSE000035004747345516273455295
ENSE000035206937357226273573424
ENSE000035288657348963473491498
ENSE000036327527351977573520016
ENSE000036403077359940173599521
ENSE000036740307360067873600881
ENSE000037124517344796073454067
ENSE000037139617360119573601436
ENSE000037309077340862273408747
ENSE000037312287342443073424902
ENSE000037336667360218573602368
ENSE000037339947360847573608574
ENSE000037354987355026773550437
ENSE000037360097355722073557354
ENSE000037361507342645373426553
ENSE000037379227341912373419318
ENSE000037400887353482473534949
ENSE000037425557343219873432291
ENSE000037446977342285773422974
ENSE000037449017360956873609916
ENSE000037481917355897273559142
ENSE000037494207360324173603304
ENSE000038432597338583673386192

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 98.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.2199 / max 193.3725, expressed in 1725 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
209555.05291275
209564.60861479
209531.5019802
209570.6707427
209540.3859155

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233698.83gold quality
periodontal ligamentUBERON:000826698.24silver quality
cardia of stomachUBERON:000116298.07gold quality
renal medullaUBERON:000036298.02gold quality
ventral tegmental areaUBERON:000269197.90gold quality
pylorusUBERON:000116697.72gold quality
inferior vagus X ganglionUBERON:000536397.71gold quality
subthalamic nucleusUBERON:000190697.63gold quality
nippleUBERON:000203097.55gold quality
superior surface of tongueUBERON:000737197.44silver quality
superior vestibular nucleusUBERON:000722797.43gold quality
spermCL:000001997.42gold quality
lateral globus pallidusUBERON:000247697.41gold quality
trigeminal ganglionUBERON:000167597.31gold quality
endothelial cellCL:000011596.83gold quality
pericardiumUBERON:000240796.70silver quality
substantia nigra pars compactaUBERON:000196596.52silver quality
substantia nigra pars reticulataUBERON:000196696.39gold quality
vena cavaUBERON:000408796.38silver quality
pharyngeal mucosaUBERON:000035596.24silver quality
lateral nuclear group of thalamusUBERON:000273696.17silver quality
saphenous veinUBERON:000731896.11gold quality
pancreatic ductal cellCL:000207996.06gold quality
medulla oblongataUBERON:000189695.89gold quality
urethraUBERON:000005795.79gold quality
male germ cellCL:000001595.75gold quality
ponsUBERON:000098895.54silver quality
dorsal root ganglionUBERON:000004495.18silver quality
tongueUBERON:000172394.99silver quality
penisUBERON:000098994.76gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.99

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1

miRNA regulators (miRDB)

20 targeting ALMS1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548N99.9871.944170
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-1211999.8768.351653
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-561-3P99.6470.903647
HSA-MIR-4649-3P99.5666.901783
HSA-MIR-4717-3P99.0666.341072
HSA-MIR-548L99.0670.902560
HSA-MIR-76098.8166.651392
HSA-MIR-3922-5P98.7766.531059
HSA-MIR-427298.7668.741810
HSA-MIR-197297.6767.381172
HSA-MIR-3928-3P97.6166.531096
HSA-MIR-526B-5P97.4167.991074
HSA-MIR-447597.3666.95761
HSA-MIR-3059-3P96.7167.08606
HSA-MIR-365A-5P94.9163.72471
HSA-MIR-365B-5P94.9163.79470

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alstrom syndrome. (PMID:11941369)
  • Mutation of ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alstrom syndrome. (PMID:11941370)
  • Variation not associated with NIDDM. (PMID:12827243)
  • “Alstrom syndrome is an autosomal recessive disease mapped to chromosome 2p12-13. The mutation of the ALMS1 gene causes obesity…and neurosensory degeneration in Alstrom synddrome” p. 297 (PMID:14646408)
  • ALSM1 involved in central role for basal body and centrosome dysfunction in the pathogenesis of obesity, insulin resistance, and type 2 diabetes (PMID:15855349)
  • Common variations in the ALMS1 gene were not associated with type 2 diabetes in a large study of a white UK population. (PMID:16601972)
  • data may have implications for the understanding of the molecular mechanisms of ALMS1 and provides the basis for further investigation of how alternative splicing of ALMS1 contributes to the severity of the disease (PMID:17594715)
  • Data show that Alms1 is expressed at higher level in preadipocytes suggesting a role of the gene in the early phase of adipogenesis. Changes in fat cell insulin sensitivity do not imply any effect on Alms1 expression. (PMID:18506366)
  • ALMS1 gene is a marker for a progressive autosomal recessive genetic disorders affecting multiple organs. (PMID:19091203)
  • By reporting four novel alleles, we use Alstrom disease to exemplify the interesting observation of allelic heterogeneity for a very rare autosomal recessive disorder in a highly inbred population. (PMID:19283855)
  • In summary, this work provides the first data on transcription factors regulating general and context-specific transcription of the disease-associated gene ALMS1. (PMID:20381594)
  • data suggest centrosomal functions for C10orf90 and KIAA1731 and new centriole-related functions for ALMS1 (PMID:20844083)
  • ALMS1-deficient fibroblasts showed a constitutively activated myofibroblast phenotype even if they do not derive from a fibrotic lesion. (PMID:21541333)
  • in a set of consanguineous patient families with Leber congenital amaurosis study identified five putative disease-causing mutations, including four novel alleles, in six families; These five mutations are located in four genes, ALMS1, IQCB1, CNGA3, and MYO7A (PMID:21901789)
  • Dilated cardiomyopathy (DCM) is one of the major manifestations of ALMS and ranges from sudden-onset infantile congestive heart failure (CHF) and DCM, which often resolves with treatment, to adult-onset cardiomyopathy (PMID:22447358)
  • a role for ALMS1 variants in the recycling endosome pathway (PMID:22693585)
  • Four mutations in ALMS1-two novel nonsense mutations in one family (p.Y1715X and p.S616X), one two previously described mutations were identified in Spanish families with Alstrom syndrome. (PMID:22876109)
  • Data show that mutations in ALMS1 were indicated in 20 of 23 subjects. (PMID:23445176)
  • Our observation broadens the clinical spectrum of Alstrom syndrome and suggests that ALMS1 mutations may be considered in patients who initially present with an acute onset of insulin-dependent diabetes (PMID:23652376)
  • The purpose of this study was to identify ALMS1 mutations and to assess the clinical features of Chinese patients with Alstrom syndrome. (PMID:24049434)
  • Data indicate that representative single-nucleotide polymorphisms of the Alstrom syndrome 1 gene (ALMS1) promoter region were significantly associated with early-onset myocardial infarction (MI) in both Japanese and Korean populations. (PMID:24122612)
  • A novel ALMS1 mutation (p.Q2051X) causes Alstrom syndrome in two Japanese brothers but spares their heterozygous parents. (PMID:24319333)
  • Our study expands the clinical spectrum associated with ALMS1 mutations and supports complete ALMS1 gene sequencing in children that present with infantile cardiomyopathy and retinopathy. (PMID:24503146)
  • Data conclude that deficiency of Alstrom protein impairs postnatal cardiomyocyte cell cycle arrest. (PMID:24595103)
  • regulates Notch activation and the accumulation of receptor in late endosomes (PMID:24681783)
  • Identification of a homozygous deleterious mutation in the ALMS1 gene as the cause of mitogenic cardiomyopathy in two siblings. (PMID:24972238)
  • ALMS has a relatively high incidence in Turkey and the present study shows that the ALMS1 mutations are largely heterogeneous. In addition, 49 variants of uncertain pathogenicity were noted, and four of these were very rare. (PMID:25296579)
  • The study represents the most comprehensive mutation analysis in patients with Alstrom Syndrome, identifying the largest number of novel mutations in a single study worldwide. (PMID:25846608)
  • In this study, we have characterized the presenting ophthalmic phenotype of young children molecularly confirmed to harbor recessive homozygous ALMS1 mutations but not yet diagnosed with Alstrom syndrome. (PMID:25864795)
  • We conclude that two independent mutations in ALMS1 and DYSF cause CRD and muscular dystrophy in the studied consanguineous Israeli Arab family. (PMID:26077327)
  • ALMS1 homozygous mutation is associated with Alstrom syndrome. (PMID:26910739)
  • Two novel mutations causing phenotypic LCA and Alstrom syndrome in Saudi patients from consanguineous families expand the genotypic spectrum of congenital retinal dystrophies. (PMID:26957854)
  • DNA microarray analysis suggested that ALMS1 might be differentially expressed between Hodgkin lymphoma (HL) cells and normal tissues. (PMID:28135309)
  • Genetic study included polymerase chain reaction amplification and direct nucleotide sequencing of the entire ALMS1 gene in DNA from seven related Alstrom Syndrome patients. A homozygous single-nucleotide c.10480C>T substitution in exon 16, predicting a p.Q3494* nonsense mutation, was identified in all affected subjects (PMID:28402684)
  • Only genetic testing analysing both nonsyndromic retinal disease (RD) genes and syndromic ciliopathy genes by comprehensive panel sequencing can result in the correct diagnosis, genetically and clinically, with important implication for the physical health of the individual. (PMID:29193673)
  • After adjusting for age, there were no significant associations of kidney dysfunction with type 2 diabetes mellitus, dyslipidemia, hypertension, cardiomyopathy or portal hypertension suggesting that kidney disease in AS is a primary manifestation of the syndrome due to lack of ALMS1 protein. (PMID:30064963)
  • This review presents mechanistic details on the role of ALMS1 in several processes including endosomal trafficking, actin organisation, maintenance of centrosome cohesion and transcription. In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. This review outlines the evidence for both ciliary and extra-ciliary functions [review] (PMID:30421101)
  • Homozygous mutations in the ALMS1 gene is associated with Non-syndromic retinal dystrophy. (PMID:30488743)
  • Phenotypic and mutational spectrum of 21 Chinese patients with Alstrom syndrome. (PMID:31755649)
  • Two North American siblings who presented with a mild clinical phenotype of Alstrom syndrome were found to have novel mutations in ALMS1. These two frame-shift mutations segregated with the disease phenotype lending evidence to their pathogenicity. (PMID:31810438)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusAlms1ENSMUSG00000063810
rattus_norvegicusAlms1ENSRNOG00000022343

Paralogs (3): C10orf90 (ENSG00000154493), CEP295 (ENSG00000166004), CEP295NL (ENSG00000178404)

Protein

Protein identifiers

Centrosome-associated protein ALMS1Q8TCU4 (reviewed: Q8TCU4)

Alternative names: Alstrom syndrome protein 1

All UniProt accessions (16): Q8TCU4, A0A087WTU9, A0A087WV20, A0A494BZW1, A0A494C003, A0A494C0F1, A0A494C1N9, A0A804HI60, A0A804HIB7, A0A804HJ69, A0A804HJA5, A0A804HJW3, A0A804HKC0, A0A804HKP4, A0A804HL70, H7C1D9

UniProt curated annotations — full annotation on UniProt →

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.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Cilium basal body. Spindle pole.

Tissue specificity. Expressed in all tissues tested including adipose and pancreas. Expressed by beta-cells of the islets in the pancreas (at protein level).

Disease relevance. 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the ALMS1 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q8TCU4-11yes
Q8TCU4-22
Q8TCU4-33

RefSeq proteins (2): NP_001365383, NP_055935 (=MANE)

Domains & families (InterPro)

IDNameType
IPR029299ALMS_motifDomain
IPR040972ALMS_repeatRepeat

Pfam: PF15309, PF18727

UniProt features (99 total): repeat 34, region of interest 21, compositionally biased region 20, sequence variant 10, modified residue 6, sequence conflict 4, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q8TCU4 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 464, 1189, 2143, 2466, 2632, 2805

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

IDPathway
R-HSA-2565942Regulation of PLK1 Activity at G2/M Transition
R-HSA-380259Loss of Nlp from mitotic centrosomes
R-HSA-380270Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-380320Recruitment of NuMA to mitotic centrosomes
R-HSA-5620912Anchoring of the basal body to the plasma membrane
R-HSA-8854518AURKA Activation by TPX2
R-HSA-1640170Cell Cycle
R-HSA-1852241Organelle biogenesis and maintenance
R-HSA-380287Centrosome maturation
R-HSA-453274Mitotic G2-G2/M phases
R-HSA-5617833Cilium Assembly
R-HSA-68877Mitotic Prometaphase
R-HSA-68886M Phase
R-HSA-69275G2/M Transition
R-HSA-69278Cell Cycle, Mitotic

MSigDB gene sets: 462 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, EFC_Q6, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GOBP_REGULATION_OF_CENTRIOLE_REPLICATION, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_CENTRIOLE_ASSEMBLY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_ACTIN_FILAMENT_ORGANIZATION, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (4): endosomal transport (GO:0016197), regulation of centriole replication (GO:0046599), regulation of stress fiber assembly (GO:0051492), positive regulation of cold-induced thermogenesis (GO:0120162)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (13): spindle pole (GO:0000922), nucleoplasm (GO:0005654), mitochondrion (GO:0005739), centrosome (GO:0005813), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630), ciliary basal body (GO:0036064), sperm end piece (GO:0097229), cytoplasm (GO:0005737), centriole (GO:0005814), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-10 pathways:

CategoryPathways
G2/M Transition3
Centrosome maturation2
Cell Cycle, Mitotic2
Loss of proteins required for interphase microtubule organization from the centrosome1
Mitotic Prometaphase1
Assembly of the 9+0 primary cilium1
Organelle biogenesis and maintenance1
M Phase1
Mitotic G2-G2/M phases1
Cell Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
microtubule organizing center3
cytoplasm2
intracellular membraneless organelle2
vesicle-mediated transport1
intracellular transport1
centriole replication1
regulation of centrosome duplication1
regulation of organelle assembly1
regulation of actin filament bundle assembly1
stress fiber assembly1
regulation of actomyosin structure organization1
positive regulation of multicellular organismal process1
cold-induced thermogenesis1
regulation of cold-induced thermogenesis1
binding1
spindle1
nuclear lumen1
intracellular membrane-bounded organelle1
centriole1
cytoskeleton1
cilium1
sperm flagellum1
intracellular anatomical structure1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

2638 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ALMS1XPNPEP3Q9NQH7831
ALMS1SLC4A5Q9BY07824
ALMS1CEP290O15078773
ALMS1DNAAF1Q8NEP3765
ALMS1BBS7Q8IWZ6741
ALMS1BBS1Q8NFJ9710
ALMS1BBS10Q8TAM1632
ALMS1RHOP08100625
ALMS1BBS2Q9BXC9617
ALMS1BBS4Q96RK4598
ALMS1BBS12Q6ZW61584
ALMS1INSP01308566
ALMS1BBS5Q8N3I7559
ALMS1ACTN4O43707521
ALMS1SLC12A1Q13621512

IntAct

124 interactions, top by confidence:

ABTypeScore
IKBKGIKBKBpsi-mi:“MI:0914”(association)0.980
CEP97CCP110psi-mi:“MI:2364”(proximity)0.950
ATG13ULK1psi-mi:“MI:2364”(proximity)0.940
MED4MED19psi-mi:“MI:2364”(proximity)0.900
BBS7BBS9psi-mi:“MI:0914”(association)0.860
MLF1DNAJB6psi-mi:“MI:0914”(association)0.750
ORFEIF3Fpsi-mi:“MI:0914”(association)0.560
CEP104CCDC66psi-mi:“MI:2364”(proximity)0.540
HSPB8VWA8psi-mi:“MI:0914”(association)0.530
FHL2CNOT1psi-mi:“MI:0914”(association)0.530
DISC1AP4M1psi-mi:“MI:0914”(association)0.530
TFDP3E2F3psi-mi:“MI:0914”(association)0.530
SKP2DPYSL4psi-mi:“MI:0914”(association)0.530
MLF1NDC80psi-mi:“MI:0914”(association)0.530
DYSFALMS1psi-mi:“MI:0403”(colocalization)0.500
DYSFALMS1psi-mi:“MI:2364”(proximity)0.500
POC1ATXNDC9psi-mi:“MI:0914”(association)0.480
GSK3BSEC16Apsi-mi:“MI:2364”(proximity)0.420
H2AC4ALMS1psi-mi:“MI:0915”(physical association)0.400
ALMS1GTF2IRD1psi-mi:“MI:0915”(physical association)0.370
MEGF10ALMS1psi-mi:“MI:0915”(physical association)0.370
LACC1FLJ10842psi-mi:“MI:0914”(association)0.350
NS1ESYT2psi-mi:“MI:0914”(association)0.350
NS1psi-mi:“MI:0914”(association)0.350

BioGRID (214): ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), ALMS1 (Synthetic Growth Defect), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS), ALMS1 (Proximity Label-MS)

ESM2 similar proteins: A0A0P0XCU3, A0A1P8BH59, A1YFC1, A1YGK6, A2T7F2, A6NJ88, B7SY83, F1QU13, F4HXQ7, F4ICX9, F4INW9, F4KCE9, O04251, O81472, O96001, P0CV01, P0CV36, P0CV42, P0CV43, P0CV45, P0CV46, P0CV55, P0CV57, P0CV58, P10322, P16531, P48786, Q0DVU4, Q10P83, Q2EI21, Q3URU2, Q5JY77, Q5QNA6, Q5R7U0, Q5SRN2, Q5U4C1, Q5XPK0, Q6K5K2, Q7T2B3, Q8N3K9

Diamond homologs: D2J0Y4, Q8K4E0, Q8TCU4, Q96M02

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 155 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Loss of Nlp from mitotic centrosomes915.0×1e-06
Loss of proteins required for interphase microtubule organization from the centrosome915.0×1e-06
AURKA Activation by TPX2914.4×1e-06
Regulation of PLK1 Activity at G2/M Transition1013.4×1e-06
Recruitment of mitotic centrosome proteins and complexes912.9×2e-06
Recruitment of NuMA to mitotic centrosomes1012.3×1e-06
Anchoring of the basal body to the plasma membrane1011.9×1e-06
Translocation of SLC2A4 (GLUT4) to the plasma membrane69.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
centriole replication843.1×5e-09
centrosome duplication534.4×8e-05
positive regulation of autophagy812.2×8e-05
autophagosome assembly711.6×4e-04
intracellular protein localization107.7×1e-04
cilium assembly105.4×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

7452 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic635
Likely pathogenic297
Uncertain significance3101
Likely benign2628
Benign88

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1033321NM_001378454.1(ALMS1):c.2464C>T (p.Gln822Ter)Pathogenic
1065120NM_001378454.1(ALMS1):c.11668+1G>APathogenic
1068526NM_001378454.1(ALMS1):c.7589C>G (p.Ser2530Ter)Pathogenic
1068901NM_001378454.1(ALMS1):c.6528dup (p.Gln2177fs)Pathogenic
1069142NM_001378454.1(ALMS1):c.1910del (p.Pro637fs)Pathogenic
1069267NM_001378454.1(ALMS1):c.1348G>T (p.Glu450Ter)Pathogenic
1070273NC_000002.11:g.(?73659316)(73659429_?)delPathogenic
1070274NC_000002.11:g.(?73716751)(73747153_?)delPathogenic
1070275NC_000002.11:g.(?73746892)(73762086_?)delPathogenic
1070276NC_000002.11:g.(?73777384)(73800561_?)delPathogenic
1070448NM_001378454.1(ALMS1):c.9442C>T (p.Gln3148Ter)Pathogenic
1070537NM_001378454.1(ALMS1):c.149del (p.Ala50fs)Pathogenic
1070538NM_001378454.1(ALMS1):c.2225_2226dup (p.Val743fs)Pathogenic
1070819NM_001378454.1(ALMS1):c.1447G>T (p.Gly483Ter)Pathogenic
1071197NM_001378454.1(ALMS1):c.870del (p.Ser290fs)Pathogenic
1071827NM_001378454.1(ALMS1):c.211G>T (p.Glu71Ter)Pathogenic
1071882NM_001378454.1(ALMS1):c.4144_4147del (p.Ser1382fs)Pathogenic
1071883NM_001378454.1(ALMS1):c.4210G>T (p.Glu1404Ter)Pathogenic
1071884NM_001378454.1(ALMS1):c.4715C>G (p.Ser1572Ter)Pathogenic
1071885NM_001378454.1(ALMS1):c.8653C>T (p.Arg2885Ter)Pathogenic
1071886NM_001378454.1(ALMS1):c.10558_10561del (p.Asp3520fs)Pathogenic
1071887NM_001378454.1(ALMS1):c.10385-2A>GPathogenic
1071888NM_001378454.1(ALMS1):c.10750C>T (p.Gln3584Ter)Pathogenic
1072014NM_001378454.1(ALMS1):c.8109del (p.Ser2704fs)Pathogenic
1072195NM_001378454.1(ALMS1):c.2071C>T (p.Gln691Ter)Pathogenic
1072503NM_001378454.1(ALMS1):c.3523dup (p.Thr1175fs)Pathogenic
1072647NM_001378454.1(ALMS1):c.2370_2371del (p.Ala792fs)Pathogenic
1073232NM_001378454.1(ALMS1):c.638dup (p.Leu214fs)Pathogenic
1073409NM_001378454.1(ALMS1):c.7405G>T (p.Glu2469Ter)Pathogenic
1073658NM_001378454.1(ALMS1):c.10619_10622del (p.Thr3540fs)Pathogenic

SpliceAI

4633 predictions. Top by Δscore:

VariantEffectΔscore
2:73386189:GAAG:Gdonor_gain1.0000
2:73386191:AGG:Adonor_loss1.0000
2:73386192:GGT:Gdonor_loss1.0000
2:73386193:G:GCdonor_loss1.0000
2:73386194:T:Gdonor_loss1.0000
2:73419114:T:Gacceptor_gain1.0000
2:73419121:A:AGacceptor_gain1.0000
2:73419122:G:Aacceptor_loss1.0000
2:73419122:G:GAacceptor_gain1.0000
2:73419122:GA:Gacceptor_gain1.0000
2:73419122:GAA:Gacceptor_gain1.0000
2:73419122:GAAA:Gacceptor_gain1.0000
2:73419122:GAAAA:Gacceptor_gain1.0000
2:73419276:G:GGdonor_gain1.0000
2:73419315:C:Gdonor_gain1.0000
2:73419315:CTAG:Cdonor_loss1.0000
2:73419318:GGT:Gdonor_loss1.0000
2:73419319:G:GAdonor_loss1.0000
2:73422855:A:AGacceptor_gain1.0000
2:73422856:G:GGacceptor_gain1.0000
2:73422856:GTC:Gacceptor_gain1.0000
2:73424428:AGG:Aacceptor_gain1.0000
2:73424429:GGG:Gacceptor_gain1.0000
2:73424429:GGGGA:Gacceptor_gain1.0000
2:73519768:T:TAacceptor_gain1.0000
2:73519769:G:Aacceptor_gain1.0000
2:73519773:A:AGacceptor_gain1.0000
2:73519773:AG:Aacceptor_loss1.0000
2:73519774:G:GAacceptor_gain1.0000
2:73519774:GA:Gacceptor_gain1.0000

AlphaMissense

27224 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:73573246:T:CL3790P0.996
2:73602212:T:CF4048L0.996
2:73602214:C:AF4048L0.996
2:73602214:C:GF4048L0.996
2:73573257:T:CF3794L0.995
2:73573259:T:AF3794L0.995
2:73573259:T:GF3794L0.995
2:73608489:T:CL4126P0.994
2:73602234:G:CR4055P0.993
2:73608557:G:CA4149P0.993
2:73602192:T:CL4041P0.992
2:73602213:T:CF4048S0.992
2:73572681:T:AW3602R0.991
2:73572681:T:CW3602R0.991
2:73602246:T:CL4059P0.991
2:73608549:G:CR4146P0.991
2:73572763:T:CL3629P0.990
2:73602205:A:CR4045S0.990
2:73602205:A:TR4045S0.990
2:73601203:T:AW3961R0.989
2:73601203:T:CW3961R0.989
2:73453332:G:CA2269P0.988
2:73602188:T:CS4040P0.988
2:73602204:G:CR4045T0.988
2:73572772:T:CL3632S0.987
2:73572763:T:AL3629H0.986
2:73602213:T:GF4048C0.986
2:73602243:G:CR4058P0.986
2:73534937:A:CS3299R0.985
2:73534939:C:AS3299R0.985

dbSNP variants (sampled 300 via entrez): RS1000010393 (2:73479675 G>C), RS1000011452 (2:73444731 G>C), RS1000017182 (2:73480089 ATTATAC>A), RS1000024872 (2:73513994 TAAAAG>T), RS1000026507 (2:73606505 T>C), RS1000027192 (2:73558261 A>G), RS1000038452 (2:73557955 C>T), RS1000062302 (2:73591630 T>C), RS1000082140 (2:73479478 G>A), RS1000102193 (2:73397888 A>C,G,T), RS1000103545 (2:73438748 CAG>C), RS1000111491 (2:73383892 C>T), RS1000123575 (2:73436247 C>T), RS1000130609 (2:73531945 G>C), RS1000166871 (2:73593466 G>A)

Disease associations

OMIM: gene MIM:606844 | disease phenotypes: MIM:203800, MIM:268000, MIM:204000, MIM:209900, MIM:312080, MIM:108300, MIM:190685, MIM:120970

GenCC curated gene-disease

DiseaseClassificationInheritance
Alstrom syndromeDefinitiveUnknown

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Alstrom syndromeDefinitiveAR

Mondo (17): Alstrom syndrome (MONDO:0008763), inherited retinal dystrophy (MONDO:0019118), hearing loss disorder (MONDO:0005365), retinitis pigmentosa (MONDO:0019200), intellectual disability (MONDO:0001071), Leber congenital amaurosis (MONDO:0018998), optic atrophy (MONDO:0003608), Bardet-Biedl syndrome (MONDO:0015229), monogenic diabetes (MONDO:0015967), primary ovarian failure (MONDO:0005387), end stage renal failure (MONDO:0004375), leukodystrophy (MONDO:0019046), cardiomyopathy (MONDO:0004994), Stickler syndrome (MONDO:0019354), Down syndrome (MONDO:0008608)

Orphanet (13): Alström syndrome (Orphanet:64), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791), Leber congenital amaurosis (Orphanet:65), Bardet-Biedl syndrome (Orphanet:110), Rare genetic diabetes mellitus (Orphanet:183625), Leukodystrophy (Orphanet:68356), Rare cardiomyopathy (Orphanet:167848), Stickler syndrome (Orphanet:828), Down syndrome (Orphanet:870), Cone rod dystrophy (Orphanet:1872), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658), NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

144 total (30 of 144 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000009Functional abnormality of the bladder
HP:0000010Recurrent urinary tract infections
HP:0000012Urinary urgency
HP:0000016Urinary retention
HP:0000020Urinary incontinence
HP:0000054Micropenis
HP:0000083Renal insufficiency
HP:0000099Glomerulonephritis
HP:0000123Nephritis
HP:0000147Polycystic ovaries
HP:0000164Abnormality of the dentition
HP:0000230Gingivitis
HP:0000311Round face
HP:0000388Otitis media
HP:0000407Sensorineural hearing impairment
HP:0000408Progressive sensorineural hearing impairment
HP:0000490Deeply set eye
HP:0000505Visual impairment
HP:0000518Cataract
HP:0000523Subcapsular cataract
HP:0000543Optic disc pallor
HP:0000548Cone/cone-rod dystrophy
HP:0000556Retinal dystrophy
HP:0000572Visual loss
HP:0000580Pigmentary retinopathy
HP:0000613Photophobia
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000729Autistic behavior

GWAS associations

75 associations (top):

StudyTraitp-value
GCST000649_14Chronic kidney disease5.000000e-14
GCST000651_1Creatinine levels1.000000e-15
GCST001220_3Metabolite levels1.000000e-11
GCST002119_2Metabolite levels (X-11787)1.000000e-23
GCST002364_1Urinary metabolites (H-NMR features)6.000000e-17
GCST002364_2Urinary metabolites (H-NMR features)5.000000e-161
GCST002364_3Urinary metabolites (H-NMR features)1.000000e-17
GCST003372_11Glomerular filtration rate (creatinine)8.000000e-20
GCST003401_32Glomerular filtration rate in non diabetics (creatinine)3.000000e-16
GCST003790_15Glomerular filtration rate5.000000e-12
GCST003790_33Glomerular filtration rate3.000000e-08
GCST003993_8Menarche (age at onset)2.000000e-08
GCST003994_1Age at voice drop1.000000e-08
GCST005316_333Intelligence (MTAG)5.000000e-09
GCST005649_7Urinary metabolite ratios in chronic kidney disease6.000000e-18
GCST005649_8Urinary metabolite ratios in chronic kidney disease7.000000e-18
GCST005649_9Urinary metabolite ratios in chronic kidney disease2.000000e-16
GCST005651_2Urinary metabolite levels in chronic kidney disease1.000000e-11
GCST006249_11Serum metabolite levels1.000000e-149
GCST006249_110Serum metabolite levels7.000000e-36
GCST006249_12Serum metabolite levels9.000000e-149
GCST006249_13Serum metabolite levels1.000000e-77
GCST006249_35Serum metabolite levels3.000000e-37
GCST006249_51Serum metabolite levels9.000000e-22
GCST006249_52Serum metabolite levels5.000000e-11
GCST006249_55Serum metabolite levels2.000000e-56
GCST006249_56Serum metabolite levels1.000000e-54
GCST006249_62Serum metabolite levels7.000000e-24
GCST006249_77Serum metabolite levels7.000000e-33
GCST006879_10Blood metabolite levels6.000000e-09

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004725metabolite measurement
EFO:0005276hydroxy-leucine measurement
EFO:0005116urinary metabolite measurement
EFO:0004703age at menarche
EFO:0007888age at voice drop
EFO:0004337intelligence
EFO:0004612high density lipoprotein cholesterol measurement

MeSH disease descriptors (13)

DescriptorNameTree numbers
D056769Alstrom SyndromeC10.500.300.099; C10.574.500.495.099; C10.668.829.800.300.099; C11.270.684.249; C16.131.077.245.063; C16.131.666.300.099; C16.320.184.063; C16.320.290.684.249; C16.320.400.375.099
D020788Bardet-Biedl SyndromeC10.228.140.617.200; C11.270.684.624; C16.131.077.245.125; C16.320.184.125
D009202CardiomyopathiesC14.280.238
D000071700Cone-Rod DystrophiesC11.270.152; C11.768.585.658.250; C16.320.290.152
D004314Down SyndromeC10.597.606.360.220; C16.131.077.327; C16.131.260.260; C16.320.180.260
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D057130Leber Congenital AmaurosisC11.270.516; C11.768.364
D009404Nephrotic SyndromeC12.050.351.968.419.630.643; C12.200.777.419.630.643; C12.950.419.630.643
D009896Optic AtrophyC10.292.700.225; C11.640.451
D016649Primary Ovarian InsufficiencyC12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750
D058499Retinal DystrophiesC11.768.585.658
D012174Retinitis PigmentosaC11.270.684; C11.768.585.658.500; C16.320.290.684

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

50 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression3
Aflatoxin B1decreases expression3
Tetrachlorodibenzodioxindecreases expression2
Tobacco Smoke Pollutiondecreases expression2
Tretinoindecreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
2,4,6-tribromophenoldecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
lead acetateaffects cotreatment, increases expression1
testosterone undecanoateaffects cotreatment, decreases expression1
decabromobiphenyl etherdecreases expression1
arsenitedecreases reaction, affects binding1
zinc protoporphyrinincreases expression, affects cotreatment1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
tetrabromobisphenol Adecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
tamibarotenedecreases expression1
di-n-butylphosphoric acidaffects expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153increases expression1
jinfukangdecreases expression, increases reaction1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Caffeineaffects phosphorylation1

Cellosaurus cell lines

2 cell lines: 2 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A1DFFDCHi003-AInduced pluripotent stem cellMale
CVCL_A1DGFDCHi003-A-1Induced pluripotent stem cellMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT03746522PHASE3COMPLETEDSetmelanotide (RM-493), Melanocortin-4 Receptor (MC4R) Agonist, in Bardet-Biedl Syndrome (BBS) and Alström Syndrome (AS) Participants With Moderate to Severe Obesity
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT03763227PHASE2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT05902962PHASE1COMPLETEDSAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872PHASE1RECRUITINGThe Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826PHASE1COMPLETEDMAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04041440PHASE1COMPLETEDSpeech Recognition Training in Children With Hearing Loss
NCT07218913PHASE1RECRUITINGTesting the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors
NCT03184584PHASE2/PHASE3TERMINATEDOpen-Label Rollover Study of PBI 4050 in Subjects With Alström Syndrome