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    SMARCAL1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 [ Homo sapiens (human) ]

    Gene ID: 50485, updated on 7-Apr-2024

    Summary

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    Official Symbol
    SMARCAL1provided by HGNC
    Official Full Name
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 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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    Location:
    2q35
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (216412484..216483053)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (216894907..216965465)
    105.20220307 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. Different Phenotypes of Schimke Immuno-Osseous Dysplasia (SIOD) in Two Sisters with the Same Mutation in the SMARCAL1 Gene. Castellano-Martinez A, et al. Endocr Metab Immune Disord Drug Targets, 2022. PMID 35209826
    2. SMARCAL1 loss and alternative lengthening of telomeres (ALT) are enriched in giant cell glioblastoma. Brosnan-Cashman JA, et al. Mod Pathol, 2021 Oct. PMID 34103668
    3. A patient with Silver-Russell syndrome with multilocus imprinting disturbance, and Schimke immuno-osseous dysplasia unmasked by uniparental isodisomy of chromosome 2. Hara-Isono K, et al. J Hum Genet, 2021 Nov. PMID 34031513
    4. SMARCAL1, the annealing helicase and the transcriptional co-regulator. Bansal R, et al. IUBMB Life, 2020 Oct. PMID 32754981
    5. Inducible SMARCAL1 knockdown in iPSC reveals a link between replication stress and altered expression of master differentiation genes. Pugliese GM, et al. Dis Model Mech, 2019 Oct 17. PMID 31515241, Free PMC Article

    See all (94) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. SMARCAL1, the annealing helicase and the transcriptional co-regulator.
      Title: SMARCAL1, the annealing helicase and the transcriptional co-regulator.
    6. 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.
    7. 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.
    8. 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.
    9. Downregulation of SMARCAL1 and BRG1 results in downregulation of ATM and ATR and therefore, mitotic abnormalities.
      Title: Regulation of ATM and ATR by SMARCAL1 and BRG1.
    10. Mcm10 is a potent DNA strand-annealing protein that inhibits fork regression by SMARCAL1.
      Title: Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression.
    Submit: New GeneRIF Correction See all GeneRIFs (52)

    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)

    Genotypes

    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 chromatin remodeler activity 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 chromatin remodeling IEA
    Inferred from Electronic Annotation
    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
    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_2023_10

    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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