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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 31-Mar-2024

Summary

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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; 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
mouse all
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Genomic context

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Location:
4q22.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (94207608..94291292)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (97523080..97606799)
105.20220307 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

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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. Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1. Loh AYT, et al. Br J Dermatol, 2021 Jun. PMID 33400266
  2. SMARCAD1 in Breast Cancer Progression. Arafat K, et al. Cell Physiol Biochem, 2018. PMID 30308496
  3. SMARCAD1 Haploinsufficiency Underlies Huriez Syndrome and Associated Skin Cancer Susceptibility. Günther C, et al. J Invest Dermatol, 2018 Jun. PMID 29409814
  4. SMARCAD1 knockdown uncovers its role in breast cancer cell migration, invasion, and metastasis. Al Kubaisy E, et al. Expert Opin Ther Targets, 2016 Sep. PMID 27232533
  5. Genome-wide linkage analysis and whole-genome sequencing identify a recurrent SMARCAD1 variant in a unique Chinese family with Basan syndrome. Li M, et al. Eur J Hum Genet, 2016 Aug. PMID 26932190, Free PMC Article

See all (75) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Basan syndrome in a family from South India: a novel SMARCAD1 variant.
    Title: Basan syndrome in a family from South India: a novel SMARCAD1 variant.
  2. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
    Title: The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
  3. MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
    Title: MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
  4. Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
    Title: Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
  5. SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLalpha to MutSalpha on damaged chromatin induces apoptosis in human cells.
    Title: SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLα to MutSα on damaged chromatin induces apoptosis in human cells.
  6. A structural model of the KAP1 RBCC domain-SMARCAD1 CUE1 domain complex is presented. SMARCAD1 CUE1 has higher affinity for KAP1 RBCC than monoubiquitin. CUE1 binds an exposed coiled-coil surface on KAP1, not a domain resembling ubiquitin.
    Title: A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin.
  7. Whole-genome sequencing on DNA from affected individuals with Huriez syndrome from three families revealed three not previously reported SNPs in SMARCAD1 gene. Western blot experiments confirmed the reduced expression of Smarcad1 protein in keratinocytes and fibroblasts from patients compared with healthy controls. Study concluded that haploinsufficiency for the skin-specific SMARCAD1 isoform accounts for Huriez syndrome.
    Title: SMARCAD1 Haploinsufficiency Underlies Huriez Syndrome and Associated Skin Cancer Susceptibility.
  8. Data suggest that retention of SMARCAD1 in nucleus is dependent on interaction of CUE1 domain of SMARCAD1 with RBCC domain of KAP1; these studies were conducted with recombinant proteins expressed in mouse embryonic stem cell line and human somatic cell line. (SMARCAD1 = ATP-dependent helicase-1; KAP1 = KRAB-interacting protein-1)
    Title: The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.
  9. SMARCAD1 knockdown resulted in a significant decrease in breast cancer cell proliferation and colony formation, leading to the significant inhibition of tumour growth in both the chick embryo and nude mouse xenograft models. This inhibition was due, at least in part, to a decrease in IKKbeta expression.
    Title: SMARCAD1 in Breast Cancer Progression.
  10. identifies Smarcad1/Fun30 as an accessory factor for the mismatch repair reaction
    Title: Nucleosomes around a mismatched base pair are excluded via an Msh2-dependent reaction with the aid of SNF2 family ATPase Smarcad1.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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

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

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

  • 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 activity, acting on DNA IBA
Inferred from Biological aspect of Ancestor
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 chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA double-strand break processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 regulation of DNA recombination IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
part_of 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

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Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
Names
ATP-dependent helicase 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)

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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_031945.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001128429.3 → NP_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:318 → 362
    Pox_D5; Poxvirus D5 protein-like
    cl26465
    Location:476 → 1000
    SNF2_N; SNF2 family N-terminal domain

  2. NM_001128430.2 → NP_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:318 → 362
    Pox_D5; Poxvirus D5 protein-like
    cl26465
    Location:476 → 1000
    SNF2_N; SNF2 family N-terminal domain

  3. NM_001254949.2 → NP_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:46 → 568
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:67 → 249
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  4. NM_001375855.1 → NP_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:476 → 998
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:497 → 679
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  5. NM_001375856.1 → NP_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:476 → 998
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:497 → 679
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  6. NM_001375857.1 → NP_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:475 → 997
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:496 → 678
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  7. NM_001375858.1 → NP_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:476 → 991
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:497 → 672
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  8. NM_001375859.1 → NP_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:46 → 570
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:67 → 249
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

  9. NM_020159.5 → NP_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:476 → 998
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:497 → 679
    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_2023_10

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_024454154.2 → XP_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:318 → 362
    Pox_D5; Poxvirus D5 protein-like
    cl26465
    Location:476 → 1000
    SNF2_N; SNF2 family N-terminal domain

  2. XM_047415987.1 → XP_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_054350548.1 → XP_054206523.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

  2. XM_054350549.1 → XP_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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H4L7.2 GenPept UniProtKB/Swiss-Prot:Q9H4L7

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