SLC7A6
protein-codingsolute carrier family 7 member 6, the group of Solute carrier family 7
Gene summary
Enables L-lysine:L-arginine antiporter activity and arginine binding activity. Involved in amino acid import across plasma membrane and carboxylic acid transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~37.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC7A6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003983.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 4 | ||||
| missense | 46 | 4 | 3 | 53 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 48 | 8 | 3 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003974.3 | 9 | MANE Select | |
| Ensembl | ENSP00000219343.6 | 9 | MANE Select | |
| RefSeq | NP_001070253.1 | 9 | Standard | |
| Ensembl | ENSP00000368448.3 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Polythiazide Action Pathway
- Methyclothiazide Action Pathway
- Bumetanide Action Pathway
- Spironolactone Action Pathway
- Eplerenone Action Pathway
Biological Process
- amino acid transmembrane transport
- cellular amino acid metabolic process
- leukocyte migration
- protein-containing complex assembly
- L-alpha-amino acid transmembrane transport
Molecular Function
- amino acid transmembrane transporter activity
- L-amino acid transmembrane transporter activity
- antiporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- basolateral plasma membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000566454
- Coding exons
- 9
- Length
- 37290
- Individuals with no LoFs
- 125672
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 76
- Defined
- 125748
- p
- 0.000302
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 229 | 294 | 0.780 | 0.0000167 | 3334 |
| Missense (PolyPhen) | 69 | 113.45 | 0.60821 | 1324 | ||
| Synonymous | -0.898 | 134 | 121 | 1.10 | 0.00000743 | 1093 |
| Loss of Function | 2.70 | 7 | 20.1 | 0.349 | 8.63e-7 | 238 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.0034 | 0.0034 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00021 | 0.00021 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the sodium-independent uptake of dibasic amino acids and sodium-dependent uptake of some neutral amino acids. Requires coexpression with SLC3A2/4F2hc to mediate the uptake of arginine, leucine and glutamine. Also acts as an arginine/glutamine exchanger, following an antiport mechanism for amino acid transport, influencing arginine release in exchange for extracellular amino acids. Plays a role in nitric oxide synthesis in human umbilical vein endothelial cells (HUVECs) via transport of L-arginine. Involved in the transport of L-arginine in monocytes. Reduces uptake of ornithine in retinal pigment epithelial (RPE) cells. {ECO:0000269|PubMed:10903140, ECO:0000269|PubMed:11311135, ECO:0000269|PubMed:14603368, ECO:0000269|PubMed:15280038, ECO:0000269|PubMed:16785209, ECO:0000269|PubMed:17197568, ECO:0000269|PubMed:17329401, ECO:0000269|PubMed:9829974}.;
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- LoFtool
- 0.184
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.508
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |