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

    Gene ID: 259173, updated on 2-Nov-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
    Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in endosomal transport. Predicted to act upstream of or within protein localization. Predicted to be located in cytosol. Predicted to be active in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in skin (RPKM 30.9), esophagus (RPKM 10.4) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ALS2CL in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46668995..46693679, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46685103..46709793, complement)
    RS_2024_09 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 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
    		  
    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_2024_08

    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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