SLC29A2
protein-codingsolute carrier family 29 member 2, the group of Solute carrier family 29
Gene summary
The uptake of nucleosides by transporters, such as SLC29A2, is essential for nucleotide synthesis by salvage pathways in cells that lack de novo biosynthetic pathways. Nucleoside transport also plays a key role in the regulation of many physiologic processes through its effect on adenosine concentration at the cell surface (Griffiths et al., 1997 [PubMed 9396714]).[supplied by OMIM, Nov 2008]
- ENT2
- HNP36
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.7 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 SLC29A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001532.3. 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 | 61 | 2 | 63 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 62 | 3 | 0 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001523.2 | 12 | MANE Select | |
| Ensembl | ENSP00000350024.2 | 12 | MANE Select | |
| RefSeq | NP_001287797.1 | 12 | Standard | |
| RefSeq | NP_001287798.1 | 10 | 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
- cell population proliferation
- adenine transport
- guanine transport
- nucleoside transport
Molecular Function
- nucleoside transmembrane transporter activity
Cellular Component
- nucleolus
- plasma membrane
- integral component of plasma membrane
- basolateral plasma membrane
- nuclear membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000357440
- Coding exons
- 12
- Length
- 9694
- Individuals with no LoFs
- 125658
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 90
- Defined
- 125748
- p
- 0.000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.481 | 236 | 258 | 0.916 | 0.0000155 | 2924 |
| Missense (PolyPhen) | 89 | 106.37 | 0.83668 | 1235 | ||
| Synonymous | 1.46 | 102 | 123 | 0.832 | 0.00000829 | 977 |
| Loss of Function | 0.0846 | 21 | 21.4 | 0.980 | 0.00000102 | 229 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00060 | 0.00060 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates equilibrative transport of purine, pyrimidine nucleosides and the purine base hypoxanthine. Very less sensitive than SLC29A1 to inhibition by nitrobenzylthioinosine (NBMPR), dipyridamole, dilazep and draflazine. {ECO:0000269|PubMed:9396714}.;
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- LoFtool
- 0.526
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 18.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.756
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |