U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

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_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.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous