SLC28A2
protein-codingsolute carrier family 28 member 2, the group of Solute carrier family 28
Gene summary
Enables neurotransmitter transmembrane transporter activity and nucleoside transmembrane transporter activity. Involved in neurotransmitter transport; nucleoside transport; and purine nucleobase transmembrane transport. Located in apicolateral plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.6 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 SLC28A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004212.4. 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 | 1 | ||||
| missense | 95 | 3 | 98 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 96 | 3 | 0 | 99 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004203.2 | 17 | MANE Select | |
| Ensembl | ENSP00000315006.4 | 17 | MANE Select | |
| Ensembl | ENSP00000454046.1 | 2 | Standard | |
| Ensembl | ENSP00000454074.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics
- Mercaptopurine Action Pathway
- Azathioprine Action Pathway
- Thioguanine Action Pathway
- Mercaptopurine Metabolism Pathway
Biological Process
- nucleobase-containing compound metabolic process
- purine nucleoside transmembrane transport
- nucleoside transmembrane transport
Molecular Function
- nucleoside transmembrane transporter activity
- nucleoside:sodium symporter activity
- purine nucleoside transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000347644
- Coding exons
- 17
- Length
- 23722
- Individuals with no LoFs
- 125402
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 345
- Defined
- 125748
- p
- 0.00138
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0913 | 349 | 354 | 0.986 | 0.0000176 | 4273 |
| Missense (PolyPhen) | 121 | 125.6 | 0.96341 | 1639 | ||
| Synonymous | 0.0543 | 135 | 136 | 0.994 | 0.00000723 | 1324 |
| Loss of Function | -0.889 | 38 | 32.5 | 1.17 | 0.00000138 | 404 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0065 | 0.0065 | notable |
| Finnish | 0.00092 | 0.00092 | rare |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.00079 | 0.00078 | rare |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium-dependent and purine-selective transporter. Exhibits the transport characteristics of the nucleoside transport system cif or N1 subtype (N1/cif) (selective for purine nucleosides and uridine). Plays a critical role in specific uptake and salvage of purine nucleosides in kidney and other tissues.;
Recessive Scores
- pRec
- 0.151
Intolerance Scores
- LoFtool
- 0.762
- RVIS EVS
- 0.58
- RVIS percentile EVS
- 82.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0907
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |