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SLC7A7
solute carrier family 7 member 7
SLC7A7 is located on the long (q) arm of chromosome 14, at band 14q11.2. Arm ratio per GRCh38 - banding schematic.
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Overview
SLC7A7 is located on chromosome 14 and encodes the y+L amino acid transporter 1 (y+LAT-1) protein, which plays a critical role in absorbing amino acids from the diet. This transporter works specifically with three positively charged amino acids - lysine, arginine and ornithine - that are essential building blocks for proteins throughout the body. The protein functions as part of a larger complex that spans cell membranes in the small intestine and kidney tubules.
Pathogenic variants in SLC7A7 follow an autosomal recessive inheritance pattern, meaning two altered copies are required to cause disease. When the transporter cannot work effectively, amino acids are lost through urine rather than being reabsorbed, which disrupts protein metabolism and can affect multiple organ systems. The gene is included on several NHS genomic testing panels for metabolic disorders and immunodeficiency conditions.
What the gene does
The SLC7A7 gene encodes the light subunit of the heterodimeric cationic amino acid transporter, a protein complex that facilitates the movement of positively charged amino acids across cellular membranes. The y+LAT-1 protein serves as the substrate-binding component of this transporter, recognising and attaching to lysine, arginine and ornithine molecules. This binding initiates the transport process that allows these amino acids to cross from the intestinal lumen into enterocytes, and from kidney filtrate back into the bloodstream.
The transporter operates primarily in epithelial cells lining the small intestine and renal tubules, where it prevents the loss of essential amino acids during digestion and urine formation. Without functional y+LAT-1, the body cannot efficiently reclaim these amino acids, leading to their excessive excretion. This disruption affects protein synthesis throughout the body, as lysine, arginine and ornithine are required for building new proteins and supporting various metabolic pathways, including the urea cycle that processes nitrogen waste.
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Chromosome location
SLC7A7 is located on the long arm of chromosome 14 at position 11.2, designated as 14q11.2. This chromosomal region contains multiple genes involved in metabolic and transport functions. The encoded protein comprises 511 amino acids that form the functional transporter subunit.
Protein structure
The y+LAT-1 protein contains a disordered region spanning amino acids 1-28 at its N-terminus. This unstructured segment may provide flexibility important for the protein's role in forming complexes with other transporter components. The remainder of the protein is organised to create transmembrane domains that anchor the transporter in cell membranes and facilitate the passage of amino acids across the lipid bilayer. Detailed experimental characterisation of additional functional domains is ongoing.
Key variants
Pathogenic variants in SLC7A7 impair the protein's capacity to bind or transport lysine, arginine and ornithine. A founder variant is particularly common in individuals of Finnish ancestry, reflecting population-specific genetic history. These alterations may disrupt protein production, destabilise the transporter structure, or interfere with amino acid binding, ultimately reducing the amount of functional transporter available in intestinal and kidney cells.
No pathogenic or likely-pathogenic ClinVar variants recorded yet for this gene.
Associated conditions
Variants in SLC7A7 cause lysinuric protein intolerance, an autosomal recessive metabolic disorder characterised by the body's inability to absorb certain amino acids efficiently. Affected individuals typically present in infancy or early childhood with feeding difficulties, failure to thrive, and episodes of metabolic crisis. The condition can progress to involve the lungs, immune system and kidneys if not managed appropriately. Because two altered gene copies are required for disease manifestation, carriers with one pathogenic variant generally remain asymptomatic.
Inheritance pattern
Conditions caused by pathogenic SLC7A7 variants typically follow autosomal recessive inheritance.
When both parents are carriers, each child has a 25% chance of being affected, 50% of being a carrier, and 25% of being unaffected.
UK clinical status
SLC7A7 appears on multiple NHS Genomic Medicine Service panels, reflecting its relevance to several clinical presentations. The gene holds green classification status on panels including Hyperammonaemia, Likely inborn error of metabolism (R98), Undiagnosed metabolic disorders, and Primary immunodeficiency or monogenic inflammatory bowel disease (R15). It is also listed on the Familial pulmonary fibrosis panel and was included in COVID-19 research initiatives. This broad panel representation underscores the diverse clinical features that can emerge when amino acid transport is compromised.
Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory
Frequently asked questions
What does it mean to be a carrier of an SLC7A7 variant?
Carriers have one pathogenic variant and one normal copy of SLC7A7, which typically provides sufficient transporter function to prevent symptoms. Carriers do not develop lysinuric protein intolerance but can pass the altered gene to their children.
How common are SLC7A7 variants?
Pathogenic SLC7A7 variants are rare in most populations, though carrier rates are higher in Finland due to a founder effect. The overall prevalence of lysinuric protein intolerance is estimated at fewer than 1 in 60,000 individuals worldwide.
Why is SLC7A7 on immunodeficiency testing panels?
Lysinuric protein intolerance can affect immune function, leading to recurrent infections and inflammatory complications. The disrupted amino acid metabolism may impair immune cell development and function, which is why the gene appears on panels for primary immunodeficiency and inflammatory bowel disease.
References
- Sperandeo MP, Andria G, Sebastio G. Lysinuric protein intolerance: update and extended mutation analysis of the SLC7A7 gene. Human mutation. 2008. PMID: 17764084
- Palacín M, Nunes V, Font-Llitjós M. The genetics of heteromeric amino acid transporters. Physiology (Bethesda, Md.). 2005. PMID: 15772300
- Sperandeo MP, Annunziata P, Ammendola V. Lysinuric protein intolerance: identification and functional analysis of mutations of the SLC7A7 gene. Human mutation. 2005. PMID: 15776427
- Palacín M, Bertran J, Chillarón J. Lysinuric protein intolerance: mechanisms of pathophysiology. Molecular genetics and metabolism. 2004. PMID: 15050971
- Chillarón J, Roca R, Valencia A. Heteromeric amino acid transporters: biochemistry, genetics, and physiology. American journal of physiology. Renal physiology. 2001. PMID: 11704550