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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


Reviewed October 2007

What is the official name of the SALL1 gene?

The official name of this gene is “spalt-like transcription factor 1.”

SALL1 is the gene's official symbol. The SALL1 gene is also known by other names, listed below.

What is the normal function of the SALL1 gene?

The SALL1 gene is part of a group of genes called the SALL family. These genes provide instructions for making proteins that are involved in the formation of tissues and organs during embryonic development. SALL proteins are transcription factors, which means they attach (bind) to specific regions of DNA and help control the activity of particular genes.

The exact function of the SALL1 protein is unclear. This protein is made in many tissues, including the kidneys, liver, and fetal and adult brain. Based on the effects of SALL1 mutations, researchers infer that this protein plays an important role in development of the hands (particularly the thumbs), ears, anus, kidneys, and other parts of the body before birth.

How are changes in the SALL1 gene related to health conditions?

Townes-Brocks Syndrome - caused by mutations in the SALL1 gene

More than 55 mutations in the SALL1 gene have been identified in people with Townes-Brocks syndrome. Researchers originally believed that all of these mutations prevented one copy of the gene in each cell from making any protein, resulting in a shortage of SALL1 protein during development. More recently, they found that some mutations lead to the production of an abnormally small version of the SALL1 protein that malfunctions within cells. The malfunctioning protein interferes with normal copies of the SALL1 protein, preventing them from entering the nucleus to regulate gene activity. Scientists suspect that this type of genetic change likely underlies the more severe cases of Townes-Brocks syndrome. Mutations that reduce the amount of SALL1 protein are probably responsible for milder cases of this condition.

The SALL1 gene appears to be necessary for the normal development of many different organs and tissues before birth, which helps explain why mutations in this gene can cause the varied birth defects associated with Townes-Brocks syndrome. It is uncertain, however, how SALL1 mutations result in the specific features of this condition including an obstruction of the anal opening (imperforate anus), abnormally shaped ears, and hand malformations.

Where is the SALL1 gene located?

Cytogenetic Location: 16q12.1

Molecular Location on chromosome 16: base pairs 51,135,975 to 51,152,316

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The SALL1 gene is located on the long (q) arm of chromosome 16 at position 12.1.

The SALL1 gene is located on the long (q) arm of chromosome 16 at position 12.1.

More precisely, the SALL1 gene is located from base pair 51,135,975 to base pair 51,152,316 on chromosome 16.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about SALL1?

You and your healthcare professional may find the following resources about SALL1 helpful.

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

What other names do people use for the SALL1 gene or gene products?

  • HSAL1
  • sal (Drosophila)-like 1
  • sal-like 1
  • sal-like 1 (Drosophila)
  • Sal-like protein 1
  • TBS
  • ZNF794

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding SALL1?

anus ; cell ; DNA ; embryonic ; gene ; imperforate anus ; nucleus ; obstruction ; protein ; syndrome ; transcription ; transcription factor

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Borozdin W, Steinmann K, Albrecht B, Bottani A, Devriendt K, Leipoldt M, Kohlhase J. Detection of heterozygous SALL1 deletions by quantitative real time PCR proves the contribution of a SALL1 dosage effect in the pathogenesis of Townes-Brocks syndrome. Hum Mutat. 2006 Feb;27(2):211-2. (
  • Botzenhart EM, Bartalini G, Blair E, Brady AF, Elmslie F, Chong KL, Christy K, Torres-Martinez W, Danesino C, Deardorff MA, Fryns JP, Marlin S, Garcia-Minaur S, Hellenbroich Y, Hay BN, Penttinen M, Shashi V, Terhal P, Van Maldergem L, Whiteford ML, Zackai E, Kohlhase J. Townes-Brocks syndrome: twenty novel SALL1 mutations in sporadic and familial cases and refinement of the SALL1 hot spot region. Hum Mutat. 2007 Feb;28(2):204-5. (
  • Botzenhart EM, Green A, Ilyina H, König R, Lowry RB, Lo IF, Shohat M, Burke L, McGaughran J, Chafai R, Pierquin G, Michaelis RC, Whiteford ML, Simola KO, Rösler B, Kohlhase J. SALL1 mutation analysis in Townes-Brocks syndrome: twelve novel mutations and expansion of the phenotype. Hum Mutat. 2005 Sep;26(3):282. (
  • Gene Review: Townes-Brocks Syndrome (
  • Kiefer SM, Ohlemiller KK, Yang J, McDill BW, Kohlhase J, Rauchman M. Expression of a truncated Sall1 transcriptional repressor is responsible for Townes-Brocks syndrome birth defects. Hum Mol Genet. 2003 Sep 1;12(17):2221-7. Epub 2003 Jul 15. (
  • Kohlhase J, Liebers M, Backe J, Baumann-Müller A, Bembea M, Destrée A, Gattas M, Grüssner S, Müller T, Mortier G, Skrypnyk C, Yano S, Wirbelauer J, Michaelis RC. High incidence of the R276X SALL1 mutation in sporadic but not familial Townes-Brocks syndrome and report of the first familial case. J Med Genet. 2003 Nov;40(11):e127. Erratum in: J Med Genet. 2004 Jan;41(1):74. (
  • Kohlhase J, Wischermann A, Reichenbach H, Froster U, Engel W. Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome. Nat Genet. 1998 Jan;18(1):81-3. (
  • NCBI Gene (
  • Netzer C, Rieger L, Brero A, Zhang CD, Hinzke M, Kohlhase J, Bohlander SK. SALL1, the gene mutated in Townes-Brocks syndrome, encodes a transcriptional repressor which interacts with TRF1/PIN2 and localizes to pericentromeric heterochromatin. Hum Mol Genet. 2001 Dec 15;10(26):3017-24. (


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? ( in the Handbook.

Reviewed: October 2007
Published: February 8, 2016