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


Reviewed January 2009

What is the official name of the SLC3A1 gene?

The official name of this gene is “solute carrier family 3 (amino acid transporter heavy chain), member 1.”

SLC3A1 is the gene's official symbol. The SLC3A1 gene is also known by other names, listed below.

What is the normal function of the SLC3A1 gene?

The SLC3A1 gene provides instructions for producing one part (subunit) of a protein made primarily in the kidneys. This subunit joins with another protein subunit, produced from the SLC7A9 gene, to form a transporter protein complex. During the process of urine formation in the kidneys, this protein complex absorbs particular protein building blocks (amino acids) back into the blood. In particular, the amino acids cystine, ornithine, arginine, and lysine are absorbed back into the blood through this mechanism.

Does the SLC3A1 gene share characteristics with other genes?

The SLC3A1 gene belongs to a family of genes called SLC (solute carriers).

A gene family is a group of genes that share important characteristics. Classifying individual genes into families helps researchers describe how genes are related to each other. For more information, see What are gene families? ( in the Handbook.

How are changes in the SLC3A1 gene related to health conditions?

cystinuria - caused by mutations in the SLC3A1 gene

More than 120 mutations in the SLC3A1 gene have been found to cause cystinuria. Many of these mutations alter a single DNA building block (nucleotide) or insert or delete a small number of nucleotides in the SLC3A1 gene. These changes lead to an abnormally functioning transporter protein complex, which causes certain amino acids to become concentrated in the urine. Cystine is the only amino acid that forms crystals and stones in the bladder or kidneys, leading to the signs and symptoms of cystinuria.

other disorders - caused by mutations in the SLC3A1 gene

Some people with cystinuria have large DNA deletions that remove not only the SLC3A1 gene but one or more neighboring genes. Individuals with these large DNA deletions have the signs and symptoms of cystinuria, but they can also have other features.

Deletions of the SLC3A1 gene and the neighboring PREPL gene cause hypotonia-cystinuria syndrome. In addition to cystinuria, people with this condition have low muscle tone (hypotonia) and poor feeding, which usually improves by early childhood. They may also have droopy eyelids (ptosis), an elongated head (dolichocephaly), and mild intellectual disability. Most people with this condition have short stature.

Deletions of the SLC3A1 gene, the PREPL gene, and the C2orf34 gene cause atypical hypotonia-cystinuria syndrome. In addition to the symptoms of hypotonia-cystinuria syndrome, individuals with the atypical form have mild to moderate delay in the development of mental and motor skills (psychomotor delay).

Deletions of the SLC3A1 gene, the PREPL gene, the C2orf34 gene, and the PPM1B gene cause 2p21 deletion syndrome. In addition to all the symptoms of the previous syndromes, individuals with 2p21 deletion syndrome have seizures soon after birth, moderate to severe psychomotor delay, and impairments in the process from which cells derive much of their energy (oxidative phosphorylation). People with this condition typically have a characteristic facial appearance with a prominent forehead, long eyelashes, a flat nasal bridge, and abnormally turned ears.

Where is the SLC3A1 gene located?

Cytogenetic Location: 2p16.3

Molecular Location on chromosome 2: base pairs 44,275,458 to 44,320,824

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

The SLC3A1 gene is located on the short (p) arm of chromosome 2 at position 16.3.

The SLC3A1 gene is located on the short (p) arm of chromosome 2 at position 16.3.

More precisely, the SLC3A1 gene is located from base pair 44,275,458 to base pair 44,320,824 on chromosome 2.

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

Where can I find additional information about SLC3A1?

You and your healthcare professional may find the following resources about SLC3A1 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 SLC3A1 gene or gene products?

  • amino acid transporter 1
  • ATR1
  • CSNU1
  • D2H
  • NBAT
  • RBAT
  • solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1
  • solute carrier family 3 (cystine, dibasic and neutral amino acid transporters), member 1
  • solute carrier family 3, member 1

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

What glossary definitions help with understanding SLC3A1?

acids ; amino acid ; arginine ; atypical ; carrier ; cysteine ; cystine ; deletion ; disability ; DNA ; gene ; hypotonia ; low muscle tone ; lysine ; motor ; muscle tone ; nucleotide ; oxidative phosphorylation ; phosphorylation ; protein ; psychomotor ; ptosis ; short stature ; solute ; stature ; subunit ; syndrome

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


  • Chabrol B, Martens K, Meulemans S, Cano A, Jaeken J, Matthijs G, Creemers JW. Deletion of C2orf34, PREPL and SLC3A1 causes atypical hypotonia-cystinuria syndrome. J Med Genet. 2008 May;45(5):314-8. doi: 10.1136/jmg.2007.055475. Epub 2008 Jan 30. (
  • Dello Strologo L, Pras E, Pontesilli C, Beccia E, Ricci-Barbini V, de Sanctis L, Ponzone A, Gallucci M, Bisceglia L, Zelante L, Jimenez-Vidal M, Font M, Zorzano A, Rousaud F, Nunes V, Gasparini P, Palacín M, Rizzoni G. Comparison between SLC3A1 and SLC7A9 cystinuria patients and carriers: a need for a new classification. J Am Soc Nephrol. 2002 Oct;13(10):2547-53. (
  • Fernández E, Carrascal M, Rousaud F, Abián J, Zorzano A, Palacín M, Chillarón J. rBAT-b(0,+)AT heterodimer is the main apical reabsorption system for cystine in the kidney. Am J Physiol Renal Physiol. 2002 Sep;283(3):F540-8. (
  • Font-Llitjós M, Jiménez-Vidal M, Bisceglia L, Di Perna M, de Sanctis L, Rousaud F, Zelante L, Palacín M, Nunes V. New insights into cystinuria: 40 new mutations, genotype-phenotype correlation, and digenic inheritance causing partial phenotype. J Med Genet. 2005 Jan;42(1):58-68. (
  • Goodyer P. The molecular basis of cystinuria. Nephron Exp Nephrol. 2004;98(2):e45-9. Review. (
  • Langman CB. The molecular basis of kidney stones. Curr Opin Pediatr. 2004 Apr;16(2):188-93. Review. (
  • Martens K, Heulens I, Meulemans S, Zaffanello M, Tilstra D, Hes FJ, Rooman R, François I, de Zegher F, Jaeken J, Matthijs G, Creemers JW. Global distribution of the most prevalent deletions causing hypotonia-cystinuria syndrome. Eur J Hum Genet. 2007 Oct;15(10):1029-33. Epub 2007 Jun 20. (
  • Martens K, Jaeken J, Matthijs G, Creemers JW. Multi-system disorder syndromes associated with cystinuria type I. Curr Mol Med. 2008 Sep;8(6):544-50. Review. (
  • NCBI Gene (
  • Schmidt C, Vester U, Wagner CA, Lahme S, Hesse A, Hoyer P, Lang F, Zerres K, Eggermann T; Arbeitsgemeinschaft für Pädiatrische Nephrologie. Significant contribution of genomic rearrangements in SLC3A1 and SLC7A9 to the etiology of cystinuria. Kidney Int. 2003 Nov;64(5):1564-72. (


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: January 2009
Published: February 8, 2016