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SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 [ Homo sapiens (human) ]

Gene ID: 56916, updated on 21-Dec-2019

Summary

Official Symbol
SMARCAD1provided by HGNC
Official Full Name
SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1provided by HGNC
Primary source
HGNC:HGNC:18398
See related
Ensembl:ENSG00000163104 MIM:612761
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; 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

Genomic context

See SMARCAD1 in Genome Data Viewer
Location:
4q22.3
Exon count:
30
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (94207608..94291292)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (95128759..95212443)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929210 Neighboring gene Sharpr-MPRA regulatory region 519 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
  • 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
Compare labs
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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1122, DKFZp762K2015

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleic acid binding NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ATP-dependent chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ATP-dependent chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA double-strand break processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
chromatin organization NAS
Non-traceable Author Statement
more info
PubMed 
chromatin remodeling NAS
Non-traceable Author Statement
more info
PubMed 
chromosome separation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3 deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H4 deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleotide metabolic process NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
protein homooligomerization NAS
Non-traceable Author Statement
more info
PubMed 
regulation of DNA recombination IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear matrix NAS
Non-traceable Author Statement
more info
PubMed 
nuclear replication fork IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
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

NCBI Reference Sequences (RefSeq)

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
    5001..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 (1) summary
    cl26465
    Location:46568
    SNF2_N; SNF2 family N-terminal domain
  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
  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
  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
  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
  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
  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
    Q9H4L7
    Related
    ENSP00000346217.4, ENST00000354268.8
    Conserved Domains (3) summary
    cd00046
    Location:517659
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00176
    Location:500787
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:853967
    Helicase_C; Helicase conserved C-terminal domain

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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024454154.1XP_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
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