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Aliases for SMARCAD1 Gene

Aliases for SMARCAD1 Gene

  • SWI/SNF-Related, Matrix-Associated Actin-Dependent Regulator Of Chromatin, Subfamily A, Containing DEAD/H Box 1 2 3 5
  • ATP-Dependent Helicase 1 3 4
  • SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily A Containing DEAD/H Box 1 3
  • EC 3.6.4.12 4
  • KIAA1122 4
  • EC 3.6.1 56
  • ADERM 3
  • BASNS 3
  • HHEL1 4
  • ETL1 3
  • HEL1 3

External Ids for SMARCAD1 Gene

Previous GeneCards Identifiers for SMARCAD1 Gene

  • GC04P095521
  • GC04P095587
  • GC04P095486
  • GC04P095347
  • GC04P095128
  • GC04P090866

Summaries for SMARCAD1 Gene

Entrez Gene Summary for SMARCAD1 Gene

  • 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]

GeneCards Summary for SMARCAD1 Gene

SMARCAD1 (SWI/SNF-Related, Matrix-Associated Actin-Dependent Regulator Of Chromatin, Subfamily A, Containing DEAD/H Box 1) is a Protein Coding gene. Diseases associated with SMARCAD1 include Adermatoglyphia and Basan Syndrome. Among its related pathways are PEDF Induced Signaling and AMPK Enzyme Complex Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and helicase activity.

UniProtKB/Swiss-Prot for SMARCAD1 Gene

  • DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs. Required for the restoration of heterochromatin organization after replication. Acts at replication sites to facilitate the maintenance of heterochromatin by directing H3 and H4 histones deacetylation, H3 Lys-9 trimethylation (H3K9me3) and restoration of silencing.

Gene Wiki entry for SMARCAD1 Gene

Additional gene information for SMARCAD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMARCAD1 Gene

Genomics for SMARCAD1 Gene

GeneHancer (GH) Regulatory Elements for SMARCAD1 Gene

Promoters and enhancers for SMARCAD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I094206 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.4 417 2.5 HDGF CLOCK SMAD1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 LOC101929210 SMARCAD1 GC04P094239
GH04I094253 Promoter 0.6 EPDnew 550.2 +45.7 45682 0.1 PKNOX1 SMARCAD1 GC04P094239 GC04M094330
GH04I094588 Enhancer 0.6 dbSUPER 42.2 +381.6 381638 1.2 ZBTB11 ZNF140 ZC3H11A CEBPG ZBTB8A ZNF623 ZNF781 ZNF697 ZNF555 ZNF213 SMARCAD1 PDLIM5 PIR44106 ENSG00000249951
GH04I094484 Enhancer 1.3 Ensembl ENCODE dbSUPER 17.7 +280.9 280888 7.9 TCF12 ZNF121 ELK1 FOS REST ZNF592 ATF4 MAFF SMARCA4 KLF1 PDLIM5 SMARCAD1 PIR44106
GH04I094504 Enhancer 0.4 dbSUPER 16.5 +297.3 297337 0.9 ZNF202 ZNF184 ZBTB33 SMARCAD1 PDLIM5 PIR44106
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMARCAD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMARCAD1 gene promoter:

Genomic Locations for SMARCAD1 Gene

Genomic Locations for SMARCAD1 Gene
chr4:94,207,608-94,291,292
(GRCh38/hg38)
Size:
83,685 bases
Orientation:
Plus strand
chr4:95,128,759-95,212,443
(GRCh37/hg19)

Genomic View for SMARCAD1 Gene

Genes around SMARCAD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMARCAD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMARCAD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCAD1 Gene

Proteins for SMARCAD1 Gene

  • Protein details for SMARCAD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H4L7-SMRCD_HUMAN
    Recommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
    Protein Accession:
    Q9H4L7
    Secondary Accessions:
    • B7Z799
    • Q05D56
    • Q96SX1
    • Q9H017
    • Q9H860
    • Q9NPU9
    • Q9ULU7

    Protein attributes for SMARCAD1 Gene

    Size:
    1026 amino acids
    Molecular mass:
    117402 Da
    Quaternary structure:
    • Binds to DNA preferentially in the vicinity of transcriptional start sites. Interacts with MSH2 and TRIM28. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Interacts with PCNA.
    SequenceCaution:
    • Sequence=AAH17953.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA86436.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB14759.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SMARCAD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMARCAD1 Gene

Selected DME Specific Peptides for SMARCAD1 Gene

Q9H4L7:
  • DEMGLGKT
  • NRLLLTGTP
  • MGLGKTIQ
  • AGGLGINL
  • NGILADE

Post-translational modifications for SMARCAD1 Gene

Domains & Families for SMARCAD1 Gene

Gene Families for SMARCAD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q9H4L7

UniProtKB/Swiss-Prot:

SMRCD_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with SMARCAD1: view

Function for SMARCAD1 Gene

Molecular function for SMARCAD1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs. Required for the restoration of heterochromatin organization after replication. Acts at replication sites to facilitate the maintenance of heterochromatin by directing H3 and H4 histones deacetylation, H3 Lys-9 trimethylation (H3K9me3) and restoration of silencing.

Enzyme Numbers (IUBMB) for SMARCAD1 Gene

Phenotypes From GWAS Catalog for SMARCAD1 Gene

Gene Ontology (GO) - Molecular Function for SMARCAD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding NAS 11031099
GO:0003677 DNA binding IDA,IEA 18675275
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 18675275
genes like me logo Genes that share ontologies with SMARCAD1: view
genes like me logo Genes that share phenotypes with SMARCAD1: view

Human Phenotype Ontology for SMARCAD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMARCAD1 Gene

MGI Knock Outs for SMARCAD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for SMARCAD1 Gene

Localization for SMARCAD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMARCAD1 Gene

Nucleus. Chromosome. Note=Colocalizes with PCNA at replication forks during S phase. Recruited to double-strand breaks (DSBs) sites of DNA damage.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMARCAD1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SMARCAD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin ISS --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005694 chromosome IEA --
GO:0016363 nuclear matrix NAS 11031099
genes like me logo Genes that share ontologies with SMARCAD1: view

Pathways & Interactions for SMARCAD1 Gene

genes like me logo Genes that share pathways with SMARCAD1: view

Pathways by source for SMARCAD1 Gene

Gene Ontology (GO) - Biological Process for SMARCAD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000018 regulation of DNA recombination IEP 11031099
GO:0000729 DNA double-strand break processing IMP 22960744
GO:0006281 DNA repair IEA --
GO:0006325 chromatin organization NAS 11031099
GO:0006338 chromatin remodeling NAS 21549307
genes like me logo Genes that share ontologies with SMARCAD1: view

No data available for SIGNOR curated interactions for SMARCAD1 Gene

Drugs & Compounds for SMARCAD1 Gene

(3) Drugs for SMARCAD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for SMARCAD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with SMARCAD1: view

Transcripts for SMARCAD1 Gene

Unigene Clusters for SMARCAD1 Gene

SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMARCAD1 Gene

No ASD Table

Relevant External Links for SMARCAD1 Gene

GeneLoc Exon Structure for
SMARCAD1
ECgene alternative splicing isoforms for
SMARCAD1

Expression for SMARCAD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMARCAD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMARCAD1 Gene

This gene is overexpressed in Esophagus (18.1), Fetal Liver (11.1), and Lung (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMARCAD1 Gene



Protein tissue co-expression partners for SMARCAD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMARCAD1 Gene:

SMARCAD1

SOURCE GeneReport for Unigene cluster for SMARCAD1 Gene:

Hs.410406

mRNA Expression by UniProt/SwissProt for SMARCAD1 Gene:

Q9H4L7-SMRCD_HUMAN
Tissue specificity: Isoform 1 is expressed ubiquitously. Isoform 3 is expressed mainly in skin, fibroblasts, keratinocytes and esophagus.

Evidence on tissue expression from TISSUES for SMARCAD1 Gene

  • Nervous system(4.5)
  • Kidney(4.2)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SMARCAD1 Gene

Germ Layers:
  • ectoderm
Systems:
  • integumentary
Organs:
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • skin
genes like me logo Genes that share expression patterns with SMARCAD1: view

Primer Products

No data available for mRNA differential expression in normal tissues for SMARCAD1 Gene

Orthologs for SMARCAD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMARCAD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMARCAD1 33 34
  • 99.84 (n)
dog
(Canis familiaris)
Mammalia SMARCAD1 34 33
  • 94.87 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCAD1 34 33
  • 94.65 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcad1 33
  • 89.05 (n)
mouse
(Mus musculus)
Mammalia Smarcad1 16 34 33
  • 88.73 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMARCAD1 34
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMARCAD1 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMARCAD1 34 33
  • 71.41 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCAD1 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smarcad1 33
  • 66.87 (n)
Str.11960 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.33554 33
zebrafish
(Danio rerio)
Actinopterygii LOC563175 33
  • 60.13 (n)
smarcad1 34
  • 53 (a)
OneToMany
SMARCAD1 (2 of 2) 34
  • 52 (a)
OneToMany
wufi25c01 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5000 33
fruit fly
(Drosophila melanogaster)
Insecta Etl1 33 34
  • 50.98 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009980 33
  • 37.39 (n)
worm
(Caenorhabditis elegans)
Secernentea M03C11.8 34
  • 33 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FUN30 34 36
  • 27 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12375 33
Species where no ortholog for SMARCAD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMARCAD1 Gene

ENSEMBL:
Gene Tree for SMARCAD1 (if available)
TreeFam:
Gene Tree for SMARCAD1 (if available)

Paralogs for SMARCAD1 Gene

(2) SIMAP similar genes for SMARCAD1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SMARCAD1: view

No data available for Paralogs for SMARCAD1 Gene

Variants for SMARCAD1 Gene

Sequence variations from dbSNP and Humsavar for SMARCAD1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1057519613 pathogenic, Adermatoglyphia, Basan syndrome 94,253,672(+) G/A/T intron_variant, splice_donor_variant
rs895436485 pathogenic, Basan syndrome 94,253,674(+) A/G/T intron_variant
rs200948051 uncertain-significance, not specified 94,226,232(+) G/A/T 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000013299 -- 94,238,907(+) G/A genic_upstream_transcript_variant, intron_variant
rs10000247 -- 94,252,099(+) G/A/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SMARCAD1 Gene

Variant ID Type Subtype PubMed ID
esv3601447 CNV loss 21293372
nsv1114557 CNV deletion 24896259
nsv292335 CNV deletion 16902084
nsv476565 CNV novel sequence insertion 20440878
nsv507182 OTHER sequence alteration 20534489
nsv819645 CNV gain 19587683

Variation tolerance for SMARCAD1 Gene

Residual Variation Intolerance Score: 7.42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.45; 90.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMARCAD1 Gene

Human Gene Mutation Database (HGMD)
SMARCAD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMARCAD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMARCAD1 Gene

Disorders for SMARCAD1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SMARCAD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
adermatoglyphia
  • aderm
basan syndrome
  • adermatoglyphia with congenital facial milia and acral blisters, digital contractures, and nail abnormalities
absence of fingerprints congenital milia
  • basan syndrome
epilepsy, familial temporal lobe, 1
  • etl1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SMRCD_HUMAN
  • Adermatoglyphia (ADERM) [MIM:136000]: An autosomal dominant condition characterized by the lack of epidermal ridges on the palms and soles, which results in the absence of fingerprints, and is associated with a reduced number of sweat gland openings and reduced sweating of palms and soles. {ECO:0000269 PubMed:21820097, ECO:0000269 PubMed:24909267}. Note=The disease is caused by mutations affecting the gene represented in this entry. Splice site mutations causing aberrant splicing of skin-specific isoform 3 are likely to exert a loss-of-function effect and are involved in ADERM. {ECO:0000269 PubMed:21820097, ECO:0000269 PubMed:24909267}.
  • Basan syndrome (BSNS) [MIM:129200]: An autosomal dominant form of adermatoglyphia associated with congenital facial milia, acral blistering, digital contractures, and nail abnormalities. Adermatoglyphia is defined by the lack of epidermal ridges on the palms and soles, which results in the absence of fingerprints. {ECO:0000269 PubMed:24664640, ECO:0000269 PubMed:26932190}. Note=The disease is caused by mutations affecting the gene represented in this entry. Splice site mutations causing aberrant splicing of skin-specific isoform 3 are likely to exert a loss-of-function effect and are involved in BSNS. {ECO:0000269 PubMed:24664640, ECO:0000269 PubMed:26932190}.

Additional Disease Information for SMARCAD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SMARCAD1: view

No data available for Genatlas for SMARCAD1 Gene

Publications for SMARCAD1 Gene

  1. SMARCAD1, a novel human helicase family-defining member associated with genetic instability: cloning, expression, and mapping to 4q22-q23, a band rich in breakpoints and deletion mutants involved in several human diseases. (PMID: 11031099) Adra CN … Drews R (Genomics 2000) 2 3 4 22 58
  2. Genome-wide linkage analysis and whole-genome sequencing identify a recurrent SMARCAD1 variant in a unique Chinese family with Basan syndrome. (PMID: 26932190) Li M … Yao Z (European journal of human genetics : EJHG 2016) 3 4 58
  3. Mutations in SMARCAD1 cause autosomal dominant adermatoglyphia and perturb the expression of epidermal differentiation-associated genes. (PMID: 24909267) Nousbeck J … Sprecher E (The British journal of dermatology 2014) 3 4 58
  4. The yeast Fun30 and human SMARCAD1 chromatin remodellers promote DNA end resection. (PMID: 22960744) Costelloe T … Llorente B (Nature 2012) 3 4 58
  5. Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1. (PMID: 21549307) Rowbotham SP … Mermoud JE (Molecular cell 2011) 3 4 58

Products for SMARCAD1 Gene

Sources for SMARCAD1 Gene

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