LAT2

Chr 7

linker for activation of T cells family member 2

Also known as: HSPC046, LAB, NTAL, WBSCR15, WBSCR5, WSCR5

NCBI Gene: 7462ENSG00000086730UniProt: Q9GZY6

This gene is one of the contiguous genes at 7q11.23 commonly deleted in Williams syndrome, a multisystem developmental disorder. This gene consists of at least 14 exons, and its alternative splicing generates 3 transcript variants, all encoding the same protein. [provided by RefSeq, Jul 2008]

208
ClinVar variants
162
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— LAT2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
162 Pathogenic / Likely Pathogenic· 37 VUS of 208 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.
0.83LOEUF
pLI 0.000
Z-score 2.09
OE 0.48 (0.29–0.83)
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.
-0.02Z-score
OE missense 1.01 (0.88–1.15)
145 obs / 144.2 exp
Tolerant

Tolerant to missense variation

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.0.48 (0.29–0.83)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.01 (0.88–1.15)
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.0.77
0≤1.21.6
LoF obs/exp: 9 / 18.8Missense obs/exp: 145 / 144.2Syn Z: 1.39

ClinVar Variant Classifications

208 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic156
Likely Pathogenic6
VUS37
Likely Benign8
Benign1
156
Pathogenic
6
Likely Pathogenic
37
VUS
8
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
156
0
156
Likely Pathogenic
0
0
6
0
6
VUS
0
32
5
0
37
Likely Benign
0
7
1
0
8
Benign
0
0
1
0
1
Total0391690208

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

View in ClinVar →

Protein Context — Lollipop Plot

LAT2 · 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.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Structure, Function and Pharmacology of SLC7 Family Members and Homologues.
Jeckelmann JM et al.·Chimia (Aarau)
2022Review
Identification and validation of a KRAS-macrophage-associated gene signature as prognostic biomarkers and potential therapeutic targets in melanoma.
Cai B et al.·Front Immunol
2025
LAT2 regulates glutamine-dependent mTOR activation to promote glycolysis and chemoresistance in pancreatic cancer.
Feng M et al.·J Exp Clin Cancer Res
2018
The mononuclear phagocyte system obscures the accurate diagnosis of infected joint replacements.
Manasherob R et al.·J Transl Med
2024
Pharmacological and structural insights into nanvuranlat, a selective LAT1 (SLC7A5) inhibitor, and its N-acetyl metabolite with implications for cancer therapy.
Jin C et al.·Sci Rep
2025
Renal amino acid transport systems and essential hypertension.
Pinto V et al.·FASEB J
2013Review
Pharmacodynamic analyses of LAT1 inhibitors in vitro and in vivo by targeted metabolomics reveal target-independent effects.
Morozova V et al.·Biomed Pharmacother
2025
The pathophysiological consequences of thyroid hormone transporter deficiencies: Insights from mouse models.
Heuer H et al.·Biochim Biophys Acta
2013Review
Long noncoding RNA GSTM3TV2 upregulates LAT2 and OLR1 by competitively sponging let-7 to promote gemcitabine resistance in pancreatic cancer.
Xiong G et al.·J Hematol Oncol
2019
Curcumin synergistically enhances the efficacy of gemcitabine against gemcitabine-resistant cholangiocarcinoma via the targeting LAT2/glutamine pathway.
Thongpon P et al.·Sci Rep
2024
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