GeneBe

SLC28A3

protein-coding

solute carrier family 28 member 3, the group of Solute carrier family 28

Gene summary

Nucleoside transporters, such as SLC28A3, regulate multiple cellular processes, including neurotransmission, vascular tone, adenosine concentration in the vicinity of cell surface receptors, and transport and metabolism of nucleoside drugs. SLC28A3 shows broad specificity for pyrimidine and purine nucleosides (Ritzel et al., 2001 [PubMed 11032837]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001199633.2

Inheritance

—

ClinVar variants

U:87B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr9:84,275,457-84,340,758

External References & Databases

Ensembl (ENSG00000197506)NCBI Gene (64078)OMIM (608269)HGNC:16484GenCCUniProt (Q9HAS3)AlphaFoldClinVar (SLC28A3)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~65.3 kb
Loading mutation effect viewer...

GenCC 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 SLC28A3 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 87
not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001199633.2. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
 3
missense
84
clinvar
6
clinvar
1
clinvar
 91
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00876396
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001199633.2RefSeqNP_001186562.118MANE Select
ENST00000376238.5EnsemblENSP00000365413.418MANE Select
NM_022127.3RefSeqNP_071410.118Standard
XM_011518905.3RefSeqXP_011517207.118Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics
  • Gemcitabine Pathway, Pharmacodynamics
  • Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics
  • Mercaptopurine Action Pathway
  • Azathioprine Action Pathway

Biological Process

  • pyrimidine nucleobase transport
  • purine nucleoside transmembrane transport
  • pyrimidine nucleoside transport
  • sodium ion transmembrane transport
  • pyrimidine-containing compound transmembrane transport

Molecular Function

  • nucleoside transmembrane transporter activity
  • nucleoside:sodium symporter activity
  • pyrimidine- and adenine-specific:sodium symporter activity
  • purine-specific nucleoside:sodium symporter activity

Cellular Component

  • endoplasmic reticulum membrane
  • plasma membrane
  • integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000376238
Coding exons
18
Length
65301
Individuals with no LoFs
125533
Homozygous LoFs
0
Heterozygous LoFs
215
Defined
125748
p
0.000855
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.073213790.8460.00001954514
Missense (PolyPhen)98126.70.773471551
Synonymous0.6431341440.9320.000008441336
Loss of Function0.3403638.30.9410.00000178444

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000990.00098rare
Latino/Admixed American0.000760.00075rare
Ashkenazi Jewish00.0absent
East Asian0.00470.0046notable
Finnish0.000190.00018rare
European (Non-Finnish)0.000460.00046rare
South Asian0.00100.0010notable
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Sodium-dependent, pyrimidine- and purine-selective. Involved in the homeostasis of endogenous nucleosides. Exhibits the transport characteristics of the nucleoside transport system cib or N3 subtype (N3/cib) (with marked transport of both thymidine and inosine). Employs a 2:1 sodium/nucleoside ratio. Also able to transport gemcitabine, 3'-azido-3'-deoxythymidine (AZT), ribavirin and 3-deazauridine. {ECO:0000269|PubMed:11032837, ECO:0000269|PubMed:16446384, ECO:0000269|PubMed:17140564}.;

Recessive Scores

pRec
0.117

Intolerance Scores

LoFtool
0.964
RVIS EVS
0.85
RVIS percentile EVS
88.48

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.0800

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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