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Genetics Home Reference: your guide to understanding genetic conditions
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SMARCAL1

Reviewed November 2008

What is the official name of the SMARCAL1 gene?

The official name of this gene is “SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1.”

SMARCAL1 is the gene's official symbol. The SMARCAL1 gene is also known by other names, listed below.

What is the normal function of the SMARCAL1 gene?

The SMARCAL1 gene provides instructions for producing a protein whose specific function is unknown. The SMARCAL1 protein can attach (bind) to chromatin, which is the complex of DNA and protein that packages DNA into chromosomes. Based on the function of similar proteins, the SMARCAL1 protein is thought to influence the activity (expression) of other genes through a process known as chromatin remodeling. The structure of chromatin can be changed (remodeled) to alter how tightly DNA is packaged. Chromatin remodeling is one way gene expression is regulated during development. When DNA is tightly packed, gene expression is lower than when DNA is loosely packed.

How are changes in the SMARCAL1 gene related to health conditions?

Schimke immuno-osseous dysplasia - increased risk from variations of the SMARCAL1 gene

More than 40 mutations in the SMARCAL1 gene have been found to increase the risk of Schimke immuno-osseous dysplasia. The mutations associated with Schimke immuno-osseous dysplasia disrupt the usual functions of the SMARCAL1 protein or prevent the production of any functional protein. People who have mutations that cause a complete lack of functional protein tend to have a more severe form of this disorder than those who have mutations that lead to an active but malfunctioning protein. Mutations in the SMARCAL1 gene are thought to lead to disease by affecting protein activity, protein stability, or the protein's ability to bind to chromatin. It is not clear how SMARCAL1 mutations contribute to short stature, kidney disease, and a weakened immune system in people with Schimke immuno-osseous dysplasia. In order for people with SMARCAL1 gene mutations to develop Schimke immuno-osseous dysplasia, other currently unknown genetic or environmental factors must also be present.

Where is the SMARCAL1 gene located?

Cytogenetic Location: 2q35

Molecular Location on chromosome 2: base pairs 217,277,136 to 217,347,775

The SMARCAL1 gene is located on the long (q) arm of chromosome 2 at position 35.

The SMARCAL1 gene is located on the long (q) arm of chromosome 2 at position 35.

More precisely, the SMARCAL1 gene is located from base pair 217,277,136 to base pair 217,347,775 on chromosome 2.

See How do geneticists indicate the location of a gene? (http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation) in the Handbook.

Where can I find additional information about SMARCAL1?

You and your healthcare professional may find the following resources about SMARCAL1 helpful.

  • Educational resources - Information pages
    Molecular Biology of the Cell (fourth edition, 2002): ATP-driven Chromatin Remodeling Machines Change Nucleosome Structure (http://www.ncbi.nlm.nih.gov/books/NBK26834/)
  • Gene Reviews - Clinical summary (http://www.ncbi.nlm.nih.gov/books/NBK1376/)

  • Genetic Testing Registry - Repository of genetic test information

    • GTR: Genetic tests for SMARCAL1 (http://www.ncbi.nlm.nih.gov/gtr/tests/?term=50485%5Bgeneid%5D)

You may also be interested in these resources, which are designed for genetics professionals and researchers.

  • PubMed - Recent literature (http://www.ncbi.nlm.nih.gov/pubmed?term=(SMARCAL1%5BTIAB%5D)%20AND%20english%5Bla%5D%20AND%20human%5Bmh%5D%20AND%20%22last%203600%20days%22%5Bdp%5D)
  • OMIM - Genetic disorder catalog (http://omim.org/entry/606622)

  • Research Resources - Tools for researchers

    • Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://atlasgeneticsoncology.org/Genes/GC_SMARCAL1.html)
    • Entrez Gene (http://www.ncbi.nlm.nih.gov/gene/50485)
    • GeneCards (http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id=50485)
    • HUGO Gene Nomenclature Committee (http://www.genenames.org/data/hgnc_data.php?hgnc_id=11102)

What other names do people use for the SMARCAL1 gene or gene products?

  • HARP
  • HepA-related protein
  • HHARP
  • SMAL1_HUMAN
  • SMARCA-like protein 1
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a-like 1

See How are genetic conditions and genes named? (http://ghr.nlm.nih.gov/handbook/mutationsanddisorders/naming) in the Handbook.

What glossary definitions help with understanding SMARCAL1?

actin ; chromatin ; chromatin remodeling ; DNA ; dysplasia ; gene ; gene expression ; immune system ; kidney ; protein ; short stature ; stature

You may find definitions for these and many other terms in the Genetics Home Reference Glossary (http://www.ghr.nlm.nih.gov/glossary).

References

  • Boerkoel CF, Takashima H, John J, Yan J, Stankiewicz P, Rosenbarker L, André JL, Bogdanovic R, Burguet A, Cockfield S, Cordeiro I, Fründ S, Illies F, Joseph M, Kaitila I, Lama G, Loirat C, McLeod DR, Milford DV, Petty EM, Rodrigo F, Saraiva JM, Schmidt B, Smith GC, Spranger J, Stein A, Thiele H, Tizard J, Weksberg R, Lupski JR, Stockton DW. Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia. Nat Genet. 2002 Feb;30(2):215-20. Epub 2002 Jan 22. (http://www.ncbi.nlm.nih.gov/pubmed/11799392?dopt=Abstract)
  • Deguchi K, Clewing JM, Elizondo LI, Hirano R, Huang C, Choi K, Sloan EA, Lücke T, Marwedel KM, Powell RD Jr, Santa Cruz K, Willaime-Morawek S, Inoue K, Lou S, Northrop JL, Kanemura Y, van der Kooy D, Okano H, Armstrong DL, Boerkoel CF. Neurologic phenotype of Schimke immuno-osseous dysplasia and neurodevelopmental expression of SMARCAL1. J Neuropathol Exp Neurol. 2008 Jun;67(6):565-77. doi: 10.1097/NEN.0b013e3181772777. (http://www.ncbi.nlm.nih.gov/pubmed/18520775?dopt=Abstract)
  • Elizondo LI, Cho KS, Zhang W, Yan J, Huang C, Huang Y, Choi K, Sloan EA, Deguchi K, Lou S, Baradaran-Heravi A, Takashima H, Lücke T, Quiocho FA, Boerkoel CF. Schimke immuno-osseous dysplasia: SMARCAL1 loss-of-function and phenotypic correlation. J Med Genet. 2009 Jan;46(1):49-59. doi: 10.1136/jmg.2008.060095. Epub 2008 Sep 19. (http://www.ncbi.nlm.nih.gov/pubmed/18805831?dopt=Abstract)
  • Entrez Gene (http://www.ncbi.nlm.nih.gov/gene/50485)
  • OMIM: SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN, SUBFAMILY A-LIKE PROTEIN 1 (http://omim.org/entry/606622)

 

The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? (http://ghr.nlm.nih.gov/handbook/consult/findingprofessional) in the Handbook.

 
Reviewed: November 2008
Published: May 20, 2013