SLC7A7

Chr 14

solute carrier family 7 member 7

Also known as: LAT3, LPI, MOP-2, Y+LAT1, y+LAT-1

NCBI Gene: 9056ENSG00000155465UniProt: Q9UM01

The protein encoded by this gene is the light subunit of a cationic amino acid transporter. This sodium-independent transporter is formed when the light subunit encoded by this gene dimerizes with the heavy subunit transporter protein SLC3A2. This transporter is found in epithelial cell membranes where it transfers cationic and large neutral amino acids from the cell to the extracellular space. Defects in this gene are a cause of lysinuric protein intolerance (LPI). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2011]

Primary Disease Associations & Inheritance

UniProtLysinuric protein intolerance
691
ClinVar variants
136
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SLC7A7
🧬
Gene-Disease Validity (ClinGen)
lysinuric protein intolerance · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
136 Pathogenic / Likely Pathogenic· 235 VUS of 691 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.96LOEUF
pLI 0.000
Z-score 1.71
OE 0.60 (0.39–0.96)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.48Z-score
OE missense 0.92 (0.83–1.02)
254 obs / 276.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.60 (0.39–0.96)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.92 (0.83–1.02)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 13 / 21.6Missense obs/exp: 254 / 276.7Syn Z: -0.32

ClinVar Variant Classifications

691 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic70
Likely Pathogenic66
VUS235
Likely Benign277
Benign18
Conflicting25
70
Pathogenic
66
Likely Pathogenic
235
VUS
277
Likely Benign
18
Benign
25
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
25
2
43
0
70
Likely Pathogenic
49
3
14
0
66
VUS
3
192
34
6
235
Likely Benign
0
3
94
180
277
Benign
0
1
11
6
18
Conflicting
—25
Total77201196192691

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC7A7 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

📖
GeneReview available — SLC7A7
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Frequency and spectrum of disease-causing variants in 1892 patients with suspected genetic HLH disorders.
Gadoury-Levesque V et al.·Blood Adv
2020Cohort
TTCT 1471 mutation in lysnuric protein intolerance: Clinical features of a Tunisian paediatric series.
Jbebli E et al.·Tunis Med
2024Cohort
Lysinuric protein intolerance: update and extended mutation analysis of the SLC7A7 gene.
Sperandeo MP et al.·Hum Mutat
2008Review
Single-cell to pre-clinical evaluation of Trem2, Folr2, and Slc7a7 as macrophage-associated biomarkers for atherosclerosis.
Örd T et al.·Cardiovasc Res
2025
Multiomics integration analysis identifies tumor cell-derived MIF as a therapeutic target and potentiates anti-PD-1 therapy in osteosarcoma.
Chen W et al.·J Immunother Cancer
2025
Downregulation of SLC7A7 Triggers an Inflammatory Phenotype in Human Macrophages and Airway Epithelial Cells.
Rotoli BM et al.·Front Immunol
2018
Familial hemophagocytic lymphohistiocytosis syndrome due to lysinuric protein intolerance: a patient with a novel compound heterozygous pathogenic variant in SLC7A7.
Matsukawa Y et al.·Int J Hematol
2022Case report
Overview of symptoms and treatment for lysinuric protein intolerance.
Noguchi A et al.·J Hum Genet
2019Review
Primary immune regulatory disorders (PIRD): expanding the mutation spectrum in Turkey and identification of sixteen novel variants.
Aykut A et al.·Immunol Res
2024
Two alternative promoters regulate the expression of lysinuric protein intolerance gene SLC7A7.
Puomila K et al.·Mol Genet Metab
2007
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools