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    SMARCAD1 SNF2 related chromatin remodeling ATPase with DExD box 1 [ Homo sapiens (human) ]

    Gene ID: 56916, updated on 14-Nov-2024

    Summary

    Official Symbol
    SMARCAD1provided by HGNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase with DExD box 1provided by HGNC
    Primary source
    HGNC:HGNC:18398
    See related
    Ensembl:ENSG00000163104 MIM:612761; AllianceGenome:HGNC:18398
    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
    HRZ; TYS; ETL1; HEL1; ADERM; BASNS
    Summary
    This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 8.6), testis (RPKM 7.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMARCAD1 in Genome Data Viewer
    Location:
    4q22.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (94207608..94291292)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (97523080..97606799)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (95128759..95212443)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene SMARCAD1 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 519 Neighboring gene uncharacterized LOC124900734 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95086553-95087260 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95087971-95088678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21729 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95129093-95129596 Neighboring gene high mobility group box 3 pseudogene 15 Neighboring gene hematopoietic prostaglandin D synthase Neighboring gene ribosomal protein L35a pseudogene 11

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Adermatoglyphia
    MedGen: C1852150 OMIM: 136000 GeneReviews: Not available
    not available
    Basan syndrome
    MedGen: C0406707 OMIM: 129200 GeneReviews: Not available
    not available
    Keratoderma with scleroatrophy of the extremities
    MedGen: C0406767 OMIM: 181600 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Identification of novel germline polymorphisms governing capecitabine sensitivity.
    EBI GWAS Catalog
    Meta-analysis identifies four new loci associated with testicular germ cell tumor.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1122, DKFZp762K2015

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent chromatin remodeler activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables nucleosome array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in DNA double-strand break processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in chromosome separation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of DNA recombination IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in heterochromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear replication fork IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
    Names
    ATP-dependent helicase 1
    SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
    sclerotylosis
    NP_001121901.1
    NP_001121902.1
    NP_001241878.1
    NP_001362784.1
    NP_001362785.1
    NP_001362786.1
    NP_001362787.1
    NP_001362788.1
    NP_064544.2
    XP_024309922.1
    XP_047271943.1
    XP_054206523.1
    XP_054206524.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_031945.1 RefSeqGene

      Range
      5258..88685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128429.3NP_001121901.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

      See identical proteins and their annotated locations for NP_001121901.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AL704040, AY008271, BC045534
      Consensus CDS
      CCDS47101.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000415576.2, ENST00000457823.6
      Conserved Domains (2) summary
      pfam03288
      Location:318362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:4761000
      SNF2_N; SNF2 family N-terminal domain
    2. NM_001128430.2NP_001121902.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

      See identical proteins and their annotated locations for NP_001121902.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AY008271, DA798320
      Consensus CDS
      CCDS47101.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000351947.4, ENST00000359052.8
      Conserved Domains (2) summary
      pfam03288
      Location:318362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:4761000
      SNF2_N; SNF2 family N-terminal domain
    3. NM_001254949.2NP_001241878.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform c

      See identical proteins and their annotated locations for NP_001241878.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AK301668, AL359929, AY008271
      Consensus CDS
      CCDS58914.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000423286.1, ENST00000509418.1
      Conserved Domains (2) summary
      PLN03142
      Location:46568
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:67249
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    4. NM_001375855.1NP_001362784.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Conserved Domains (2) summary
      PLN03142
      Location:476998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    5. NM_001375856.1NP_001362785.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Conserved Domains (2) summary
      PLN03142
      Location:476998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    6. NM_001375857.1NP_001362786.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:475997
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:496678
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    7. NM_001375858.1NP_001362787.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:476991
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497672
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    8. NM_001375859.1NP_001362788.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:46570
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:67249
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    9. NM_020159.5NP_064544.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      See identical proteins and their annotated locations for NP_064544.2

      Status: REVIEWED

      Source sequence(s)
      AB032948, AL704040, AY008271
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Related
      ENSP00000346217.4, ENST00000354268.9
      Conserved Domains (2) summary
      PLN03142
      Location:476998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    RNA

    1. NR_045644.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    2. NR_164722.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    3. NR_164723.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    4. NR_164724.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    5. NR_164725.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    6. NR_164726.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    7. NR_164727.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    8. NR_164728.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    9. NR_164729.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    10. NR_164730.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    11. NR_164731.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    12. NR_164732.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    13. NR_164733.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    14. NR_164734.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    15. NR_164735.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    16. NR_164736.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746
    17. NR_164737.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      94207608..94291292
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024454154.2XP_024309922.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

      Conserved Domains (2) summary
      pfam03288
      Location:318362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:4761000
      SNF2_N; SNF2 family N-terminal domain
    2. XM_047415987.1XP_047271943.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    RNA

    1. XR_007057943.1 RNA Sequence

    2. XR_007057944.1 RNA Sequence

    3. XR_007057945.1 RNA Sequence

    4. XR_007057946.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      97523080..97606799
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350548.1XP_054206523.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

    2. XM_054350549.1XP_054206524.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    RNA

    1. XR_008487016.1 RNA Sequence

    2. XR_008487017.1 RNA Sequence

    3. XR_008487018.1 RNA Sequence

    4. XR_008487019.1 RNA Sequence