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ALS2CL ALS2 C-terminal like [ Homo sapiens (human) ]

Gene ID: 259173, updated on 5-Mar-2024

Summary

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Official Symbol
ALS2CLprovided by HGNC
Official Full Name
ALS2 C-terminal likeprovided by HGNC
Primary source
HGNC:HGNC:20605
See related
Ensembl:ENSG00000178038 MIM:612402; AllianceGenome:HGNC:20605
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RN49018
Summary
Enables identical protein binding activity. Acts upstream of or within endosome organization. Predicted to be located in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in skin (RPKM 30.9), esophagus (RPKM 10.4) and 18 other tissues See more
Orthologs
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Genomic context

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Location:
3p21.31
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46668995..46693679, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46685103..46709793, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46710485..46735169, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:46615492-46616264 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:46616265-46617037 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46617811-46618582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46618583-46619356 Neighboring gene hESC enhancers GRCh37_chr3:46620129-46620901 and GRCh37_chr3:46620902-46621673 Neighboring gene cripto, EGF-CFC family member Neighboring gene NANOG hESC enhancer GRCh37_chr3:46646153-46646654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46659485-46659985 Neighboring gene family with sequence similarity 240 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46671119-46671867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46702285-46702880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46703861-46704506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46713160-46713970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46717270-46717818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46720185-46720684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46733733-46734524 Neighboring gene Sharpr-MPRA regulatory region 4085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46736106-46736895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46737985-46738484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46747903-46748660 Neighboring gene transmembrane inner ear Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19798 Neighboring gene serine protease 50

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Multiple tumor-suppressor genes on chromosome 3p contribute to head and neck squamous cell carcinoma tumorigenesis. Lee DJ, et al. Cancer Biol Ther, 2010 Oct 1. PMID 20657180, Free PMC Article
  2. Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease. Jouan L, et al. Behav Brain Funct, 2013 Feb 20. PMID 23425335, Free PMC Article
  3. ALS2CL, the novel protein highly homologous to the carboxy-terminal half of ALS2, binds to Rab5 and modulates endosome dynamics. Hadano S, et al. FEBS Lett, 2004 Sep 24. PMID 15388334
  4. ALS2CL, a novel ALS2-interactor, modulates ALS2-mediated endosome dynamics. Suzuki-Utsunomiya K, et al. Biochem Biophys Res Commun, 2007 Mar 9. PMID 17239822
  5. Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors. Feng X, et al. Sci Adv, 2022 May 13. PMID 35559673, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This supports the notion that de novo mutations in ALS2CL are extremely rare in schizophrenia
    Title: Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease.
  2. Data provide further support that ALS2CL, EPHA3, and CMYA1 are bona-fide tumor-suppressor genes and contribute to the tumorigenesis of HNSCC.
    Title: Multiple tumor-suppressor genes on chromosome 3p contribute to head and neck squamous cell carcinoma tumorigenesis.
  3. These results suggest that amyotrophic lateral sclerosis 2 C-terminal like (ALS2CL), a novel ALS2 homologue, modulates Rab5-mediated endosome dynamics in HeLa cells.
    Title: ALS2CL, the novel protein highly homologous to the carboxy-terminal half of ALS2, binds to Rab5 and modulates endosome dynamics.
  4. ALS2CL is a novel ALS2-interacting protein implicated in ALS2-mediated endosome dynamics.
    Title: ALS2CL, a novel ALS2-interactor, modulates ALS2-mediated endosome dynamics.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC129698, DKFZp686P238

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ALS2 C-terminal-like protein

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.

mRNA and Protein(s)

  1. NM_001190707.2 → NP_001177636.1  ALS2 C-terminal-like protein isoform 1

    See identical proteins and their annotated locations for NP_001177636.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC134504, AK126505, AK131270, DA242202, DB350037
    Consensus CDS
    CCDS2743.1
    UniProtKB/Swiss-Prot
    Q32MA1, Q60I27, Q6AI56, Q6ZNC5, Q6ZNC7, Q6ZTL4, Q86YD2, Q8N9U1, Q8NAL7
    Related
    ENSP00000413223.1, ENST00000415953.5
    Conserved Domains (4) summary
    COG4642
    Location:358 → 519
    COG4642; Uncharacterized conserved protein [Function unknown]
    pfam02204
    Location:834 → 938
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam02493
    Location:358 → 378
    MORN; MORN repeat
    cl17171
    Location:223 → 321
    PH-like; Pleckstrin homology-like domain

  2. NM_147129.5 → NP_667340.2  ALS2 C-terminal-like protein isoform 1

    See identical proteins and their annotated locations for NP_667340.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the same isoform (1) as variant 2.
    Source sequence(s)
    AB107015, AC134504, AK126505, DB350037
    Consensus CDS
    CCDS2743.1
    UniProtKB/Swiss-Prot
    Q32MA1, Q60I27, Q6AI56, Q6ZNC5, Q6ZNC7, Q6ZTL4, Q86YD2, Q8N9U1, Q8NAL7
    Related
    ENSP00000313670.4, ENST00000318962.9
    Conserved Domains (4) summary
    COG4642
    Location:358 → 519
    COG4642; Uncharacterized conserved protein [Function unknown]
    pfam02204
    Location:834 → 938
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam02493
    Location:358 → 378
    MORN; MORN repeat
    cl17171
    Location:223 → 321
    PH-like; Pleckstrin homology-like domain

RNA

  1. NR_033815.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC134504, AK126505, AL832132, DB350037

  2. NR_135622.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC104304, AC134504

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46668995..46693679 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46685103..46709793 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_182774.1: Suppressed sequence

    Description
    NM_182774.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.

  2. NM_182775.2: Suppressed sequence

    Description
    NM_182775.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q60I27.1 GenPept UniProtKB/Swiss-Prot:Q60I27

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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