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    SMARCAL1 SNF2 related chromatin remodeling annealing helicase 1 [ Homo sapiens (human) ]

    Gene ID: 50485, updated on 9-Dec-2024

    Summary

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    Official Symbol
    SMARCAL1provided by HGNC
    Official Full Name
    SNF2 related chromatin remodeling annealing helicase 1provided by HGNC
    Primary source
    HGNC:HGNC:11102
    See related
    Ensembl:ENSG00000138375 MIM:606622; AllianceGenome:HGNC:11102
    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
    HARP; HHARP
    Summary
    The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 7.5), testis (RPKM 7.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMARCAL1 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (216412484..216483053)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (216894907..216965465)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (217277207..217347776)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene uncharacterized LOC107985983 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:217180211-217181410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:217183431-217184162 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:217184163-217184894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217205324-217206036 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217214111-217214808 Neighboring gene SMARCAL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217256655-217257184 Neighboring gene uncharacterized LOC107985984 Neighboring gene Sharpr-MPRA regulatory region 13820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:217339556-217340056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17098 Neighboring gene RPL37A divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17100 Neighboring gene ribosomal protein L37a

    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. Novel compound mutations of SMARCAL1 associated with severe Schimke immuno-osseous dysplasia in a Chinese patient. Yue Z, et al. Nephrol Dial Transplant, 2010 May. PMID 20179009
    2. SMARCAL1 and telomeres: Replicating the troublesome ends. Poole LA, et al. Nucleus, 2016 May 3. PMID 27355316, Free PMC Article
    3. SMARCAL1 Resolves Replication Stress at ALT Telomeres. Cox KE, et al. Cell Rep, 2016 Feb 9. PMID 26832416, Free PMC Article
    4. Ligand-induced conformation changes drive ATP hydrolysis and function in SMARCAL1. Gupta M, et al. FEBS J, 2015 Oct. PMID 26195148
    5. A novel SMARCAL1 mutation associated with a mild phenotype of Schimke immuno-osseous dysplasia (SIOD). Santangelo L, et al. BMC Nephrol, 2014 Mar 3. PMID 24589093, Free PMC Article

    See all (101) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells.
      Title: CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells.
    2. Oncogenic functions and therapeutic potentials of targeted inhibition of SMARCAL1 in small cell lung cancer.
      Title: Oncogenic functions and therapeutic potentials of targeted inhibition of SMARCAL1 in small cell lung cancer.
    3. Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells.
      Title: Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells.
    4. Different Phenotypes of Schimke Immuno-Osseous Dysplasia (SIOD) in Two Sisters with the Same Mutation in the SMARCAL1 Gene.
      Title: Different Phenotypes of Schimke Immuno-Osseous Dysplasia (SIOD) in Two Sisters with the Same Mutation in the SMARCAL1 Gene.
    5. SMARCAL1 loss and alternative lengthening of telomeres (ALT) are enriched in giant cell glioblastoma.
      Title: SMARCAL1 loss and alternative lengthening of telomeres (ALT) are enriched in giant cell glioblastoma.
    6. A patient with Silver-Russell syndrome with multilocus imprinting disturbance, and Schimke immuno-osseous dysplasia unmasked by uniparental isodisomy of chromosome 2.
      Title: A patient with Silver-Russell syndrome with multilocus imprinting disturbance, and Schimke immuno-osseous dysplasia unmasked by uniparental isodisomy of chromosome 2.
    7. SMARCAL1, the annealing helicase and the transcriptional co-regulator.
      Title: SMARCAL1, the annealing helicase and the transcriptional co-regulator.
    8. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
      Title: Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
    9. SMARCAL1-deficient induced pluripotent stem cells maintain active DNA damage response beyond differentiation.
      Title: Inducible SMARCAL1 knockdown in iPSC reveals a link between replication stress and altered expression of master differentiation genes.
    10. EXD2 deficiency leads to fork collapse, hypersensitivity to replication inhibitors, and genomic instability. Impeding fork regression by inactivation of SMARCAL1 or removal of RECQ1's inhibition in EXD2(-/-) cells restores efficient fork restart and genome stability. Moreover, purified EXD2 efficiently processes substrates mimicking regressed forks.
      Title: EXD2 Protects Stressed Replication Forks and Is Required for Cell Viability in the Absence of BRCA1/2.
    Submit: New GeneRIF Correction See all GeneRIFs (54)

    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
    Schimke immuno-osseous dysplasia
    MedGen: C0877024 OMIM: 242900 GeneReviews: Schimke Immunoosseous Dysplasia
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent DNA/DNA annealing activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent DNA/DNA annealing activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables ATP-dependent activity, acting on DNA IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in replication fork processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in replication fork processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in replication fork processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in t-circle formation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of DNA replication factor A complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nuclear replication fork IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
    Names
    ATP-driven annealing helicase
    HepA-related protein
    SMARCA-like protein 1
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1
    sucrose nonfermenting protein 2-like 1
    NP_001120679.1
    NP_054859.2

    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

    1. NG_009771.1 RefSeqGene

      Range
      5001..75640
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_108

    mRNA and Protein(s)

    1. NM_001127207.2 → NP_001120679.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

      See identical proteins and their annotated locations for NP_001120679.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      BC043341, BX104166, DA856812
      Consensus CDS
      CCDS2403.1
      UniProtKB/Swiss-Prot
      A6NEH0, Q53R00, Q96AY1, Q9NXQ5, Q9NZC9, Q9UFH3, Q9UI93
      UniProtKB/TrEMBL
      A0A8V8TLD4
      Related
      ENSP00000350940.5, ENST00000358207.9
      Conserved Domains (3) summary
      COG0553
      Location:417 → 889
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      pfam07443
      Location:248 → 301
      HARP; HepA-related protein (HARP)
      pfam15759
      Location:85 → 303
      TMEM108; TMEM108 family

    2. NM_014140.4 → NP_054859.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

      See identical proteins and their annotated locations for NP_054859.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      BC043341, BX104166, DB099423
      Consensus CDS
      CCDS2403.1
      UniProtKB/Swiss-Prot
      A6NEH0, Q53R00, Q96AY1, Q9NXQ5, Q9NZC9, Q9UFH3, Q9UI93
      UniProtKB/TrEMBL
      A0A8V8TLD4
      Related
      ENSP00000349823.4, ENST00000357276.9
      Conserved Domains (3) summary
      COG0553
      Location:417 → 889
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      pfam07443
      Location:248 → 301
      HARP; HepA-related protein (HARP)
      pfam15759
      Location:85 → 303
      TMEM108; TMEM108 family

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      216412484..216483053
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      216894907..216965465
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZC9.1 GenPept UniProtKB/Swiss-Prot:Q9NZC9

    Gene LinkOut

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

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