SLC7A2
protein-codingsolute carrier family 7 member 2, the group of Solute carrier family 7
Gene summary
The protein encoded by this gene is a cationic amino acid transporter and a member of the APC (amino acid-polyamine-organocation) family of transporters. The encoded membrane protein is responsible for the cellular uptake of arginine, lysine and ornithine. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
- ATRC2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~73.5 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 SLC7A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001370338.1. 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 | 1 | 4 | 5 | |||
| missense | 99 | 7 | 2 | 108 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 100 | 7 | 6 | 113 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001357267.1 | 11 | MANE Select | |
| Ensembl | ENSP00000419140.2 | 11 | MANE Select | |
| RefSeq | NP_001008539.3 | 11 | Standard | |
| RefSeq | NP_001158243.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysine Degradation
- Hyperlysinemia I, Familial
- 2-aminoadipic 2-oxoadipic aciduria
- Pyridoxine dependency with seizures
- Saccharopinuria/Hyperlysinemia II
Biological Process
- nitric oxide production involved in inflammatory response
- cellular amino acid metabolic process
- nitric oxide biosynthetic process
- amino acid transport
- macrophage activation
Molecular Function
- L-ornithine transmembrane transporter activity
- amino acid transmembrane transporter activity
- basic amino acid transmembrane transporter activity
- arginine transmembrane transporter activity
- L-lysine transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
- cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000004531
- Coding exons
- 12
- Length
- 73486
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 46
- Defined
- 125747
- p
- 0.000183
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.41 | 477 | 398 | 1.20 | 0.0000219 | 4514 |
| Missense (PolyPhen) | 142 | 140.59 | 1.01 | 1584 | ||
| Synonymous | -1.96 | 195 | 163 | 1.20 | 0.0000109 | 1426 |
| Loss of Function | 1.50 | 21 | 29.8 | 0.704 | 0.00000140 | 364 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00061 | 0.00052 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine); the affinity for its substrates differs between isoforms created by alternative splicing. Isoform 1 functions as permease that mediates the transport of the cationic amino acids (arginine, lysine and ornithine), and it has much higher affinity for arginine than isoform 2. Isoform 2 functions as low-affinity, high capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) (PubMed:9174363). May play a role in classical or alternative activation of macrophages via its role in arginine transport. {ECO:0000250|UniProtKB:P18581, ECO:0000269|PubMed:9174363}.;
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- LoFtool
- 0.0207
- RVIS EVS
- 0.41
- RVIS percentile EVS
- 76.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.333
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |