SLC28A1

protein-coding

solute carrier family 28 member 1, the group of Solute carrier family 28

Gene summary

Enables azole transmembrane transporter activity; pyrimidine- and adenosine-specific:sodium symporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport and nucleoside transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_004213.5

Inheritance

ClinVar variants

U:91B:16

Top phenotype

Uridine-cytidineuria

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr15:84,884,654-84,945,798

External References & Databases

Ensembl (ENSG00000156222)

Transcript & Mutation Effects

hg38 • Region Span ~61.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Uridine-cytidineuriaAR

Manifestation: Biochemical

Intervention: General

Rationale: The clinical relevance is unclear

Refs: 30658162; 30847922

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC28A1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 94

SLC28A1-related disorderTotal: 15

not providedTotal: 5

Uridine-cytidineuriaTotal: 3

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004213.5. 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 clinvar	4 clinvar	4 clinvar	9
missense			87 clinvar	5 clinvar	3 clinvar	95
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	91	9	7	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 89 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004213.5	RefSeq	NP_004204.3	17	MANE Select
ENST00000394573.6	Ensembl	ENSP00000378074.1	17	MANE Select
NM_001287761.2	RefSeq	NP_001274690.1	14	Standard
NM_001287762.2	RefSeq	NP_001274691.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics
Gemcitabine Pathway, Pharmacodynamics
Capecitabine Action Pathway
Capecitabine Metabolism Pathway
Gemcitabine Action Pathway

Biological Process

nucleobase-containing compound metabolic process
pyrimidine nucleobase transport
nucleoside transport
pyrimidine-containing compound transmembrane transport
nucleoside transmembrane transport

Molecular Function

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

Cellular Component

plasma membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394573
Coding exons: 17
Length: 90992
Individuals with no LoFs: 125343
Homozygous LoFs: 2
Heterozygous LoFs: 403
Defined: 125748
p: 0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.742	393	354	1.11	0.0000224	4184
Missense (PolyPhen)		136	138.77	0.98004		1740
Synonymous	-1.65	177	151	1.17	0.0000105	1331
Loss of Function	0.389	31	33.4	0.927	0.00000174	361

Population LoF Frequency

Population	CAF	p-value	Status
African	0.014	0.014	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00099	0.00099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00010	0.000092	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.0024	0.0024	notable
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium-dependent and pyrimidine-selective. Exhibits the transport characteristics of the nucleoside transport system cit or N2 subtype (N2/cit) (selective for pyrimidine nucleosides and adenosine). It also transports the antiviral pyrimidine nucleoside analogs 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxycytidine (ddC). It may be involved in the intestinal absorption and renal handling of pyrimidine nucleoside analogs used to treat acquired immunodeficiency syndrome (AIDS). It has the following selective inhibition: adenosine, thymidine, cytidine, uridine >> guanosine, inosine.;

Recessive Scores

pRec: 0.171

Intolerance Scores

LoFtool: 0.876
RVIS EVS: 0.76
RVIS percentile EVS: 86.85

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.247

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High