ALMS1 ALMS1 centrosome and basal body associated protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALMS1provided by HGNC
Official Full Name: ALMS1 centrosome and basal body associated proteinprovided by HGNC
Primary source: HGNC:HGNC:428
See related: Ensembl:ENSG00000116127 MIM:606844; AllianceGenome:HGNC:428
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ALSS
Summary: 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]
Annotation information: Annotation category: suggests misassembly
Expression: Broad expression in testis (RPKM 15.5), ovary (RPKM 5.0) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p13.1

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (73385758..73609919)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (73398811..73623015)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (73612886..73837046)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overburden of rare ALMS1 deleterious variants in Chinese early-onset type 2 diabetes with severe insulin resistance.
Title: Overburden of rare ALMS1 deleterious variants in Chinese early-onset type 2 diabetes with severe insulin resistance.
Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.
Title: Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.
Unraveling Alstrom syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family.
Title: Unraveling Alström syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family.
Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes.
Title: Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes.
Identification of ALMS1 pathogenic variants in Chinese patients with Alstrom syndrome.
Title: Identification of ALMS1 pathogenic variants in Chinese patients with Alström syndrome.
Whole-Genome Sequencing Identifies Novel Heterozygous Mutation in ALMS1 in Three Men With Both Peyronie's and Dupuytren's Disease.
Title: Whole-Genome Sequencing Identifies Novel Heterozygous Mutation in ALMS1 in Three Men With Both Peyronie's and Dupuytren's Disease.
New pathogenic variants of ALMS1 gene in two Chinese families with Alstrom Syndrome.
Title: New pathogenic variants of ALMS1 gene in two Chinese families with Alström Syndrome.
Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alstrom syndrome.
Title: Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alström syndrome.
Prevalent ALMS1 Pathogenic Variants in Spanish Alstrom Patients.
Title: Prevalent ALMS1 Pathogenic Variants in Spanish Alström Patients.
Molecular and phenotypic investigation of a New Zealand cohort of childhood-onset retinal dystrophy.
Title: Molecular and phenotypic investigation of a New Zealand cohort of childhood-onset retinal dystrophy.

Submit: New GeneRIF Correction See all GeneRIFs (58)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Alstrom syndrome MedGen: C0268425 OMIM: 203800 GeneReviews: Alstrom Syndrome	Compare labs

EBI GWAS Catalog

Description
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. EBI GWAS Catalog EBI GWAS CatalogPubMed
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic loci influencing kidney function and chronic kidney disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links. EBI GWAS Catalog EBI GWAS CatalogPubMed
Human metabolic individuality in biomedical and pharmaceutical research. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with kidney function and chronic kidney disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
retropepsin	gag-pol	HIV-1 PR is identified to have a physical interaction with Alstrom syndrome 1 (ALMS1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-111206 (e-PCR)
- UniSTS:168219

D2S2696 (e-PCR)
- UniSTS:27435

SHGC-105060 (e-PCR)
- UniSTS:169099

D2S2608 (e-PCR)
- UniSTS:17037

D2S2065 (e-PCR)
- UniSTS:12458

RH45615 (e-PCR)
- UniSTS:88556

RH12381 (e-PCR)
- UniSTS:35830

RH98437 (e-PCR)
- UniSTS:90362

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within endosomal transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of centriole replication	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with centriole	IDA Inferred from Direct Assay more info	PubMed
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in spindle pole	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: centrosome-associated protein ALMS1

Names: Alstrom syndrome 1; Alstrom syndrome protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011690.1 RefSeqGene

Range

5001..229167

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_741

mRNA and Protein(s)

NM_001378454.1 → NP_001365383.1 centrosome-associated protein ALMS1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes isoform 2. This transcript and NM_015120.4 have the same exon combination but differ in the length of the encoded proteins.

Source sequence(s)

AC074008, AC092653, AC096546, KF573641

Consensus CDS

CCDS42697.1

UniProtKB/Swiss-Prot

A0A087WZY3, Q53S05, Q580Q8, Q86VP9, Q8TCU4, Q9Y4G4

UniProtKB/TrEMBL

A0A087WTU9

Related

ENSP00000482968.1, ENST00000613296.6

Conserved Domains (2) summary

pfam18727
Location:1770 → 1816

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:4032 → 4163

ALMS_motif; ALMS motif
NM_015120.4 → NP_055935.4 centrosome-associated protein ALMS1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1. This transcript and NM_001378454.1 have the same exon combination but differ in the length of the encoded proteins.

Source sequence(s)

AC074008, AC092653, AC096546, AJ417593

UniProtKB/TrEMBL

A0A087WTU9

Related

ENSP00000478155.1, ENST00000484298.5

Conserved Domains (2) summary

pfam06583
Location:1425 → 1573

Neogenin_C; Neogenin C-terminus

pfam15309
Location:4034 → 4165

ALMS_motif; ALMS motif