SLC28A1

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

Basic information

Region (hg38): 15:84884653-84945798

Links

ENSG00000156222 ∙ NCBI:9154 ∙ OMIM:606207 ∙ HGNC:11001 ∙ Uniprot:O00337 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Uridine-cytidineuria	AR	General	The clinical relevance is unclear	Biochemical	30658162; 30847922

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC28A1 gene.

• Inborn genetic diseases (24 variants)
• not provided (4 variants)
• Uridine-cytidineuria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC28A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	3

Variants in SLC28A1

This is a list of pathogenic ClinVar variants found in the SLC28A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-84887769-C-T		SLC28A1-related disorder	Benign (Nov 25, 2019)
15-84887830-A-C		not specified	Uncertain significance (Mar 23, 2022)
15-84887831-T-A		not specified	Uncertain significance (Mar 23, 2022)
15-84888762-C-T		SLC28A1-related disorder	Likely benign (Dec 26, 2019)
15-84888799-T-C		SLC28A1-related disorder	Benign (Nov 08, 2019)
15-84888803-G-A		SLC28A1-related disorder	Benign (Nov 13, 2019)
15-84888842-C-G		not specified	Uncertain significance (Jan 02, 2024)
15-84888842-C-T		not specified	Uncertain significance (Feb 21, 2024)
15-84894964-C-T		not specified	Uncertain significance (Dec 07, 2023)
15-84894993-G-A		not specified	Uncertain significance (Oct 06, 2021)
15-84895038-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-84895048-A-C		not specified	Uncertain significance (Mar 24, 2023)
15-84895080-C-CTTG		SLC28A1-related disorder	Benign (Oct 30, 2019)
15-84895102-G-A		SLC28A1-related disorder	Benign/Likely benign (Jan 01, 2023)
15-84895110-C-A		not specified	Uncertain significance (Aug 13, 2021)
15-84895420-C-G		SLC28A1-related disorder	Likely benign (Nov 25, 2019)
15-84904099-G-T		not specified	Uncertain significance (Jan 16, 2024)
15-84904147-A-G		not specified	Uncertain significance (Nov 07, 2023)
15-84904200-G-A		SLC28A1-related disorder	Benign (Oct 30, 2019)
15-84904203-G-T		SLC28A1-related disorder	Benign (Nov 08, 2019)
15-84904227-C-T		not specified	Uncertain significance (May 03, 2023)
15-84904236-G-A		not specified	Uncertain significance (May 11, 2022)
15-84905547-G-C		not specified	Uncertain significance (Nov 07, 2022)
15-84905565-A-T		SLC28A1-related disorder	Benign (Nov 26, 2019)
15-84905621-T-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC28A1	protein_coding	protein_coding	ENST00000394573	17	90992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.74e-20	0.00607	125343	2	403	125748	0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.742	393	354	1.11	0.0000224	4184
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0150	0.0149
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000217	0.000217
Finnish	0.000101	0.0000924
European (Non-Finnish)	0.000406	0.000404
Middle Eastern	0.000217	0.000217
South Asian	0.00242	0.00242
Other	0.00130	0.00130

dbNSFP

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.
• Pathway: Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;Capecitabine Action Pathway;Capecitabine Metabolism Pathway;Gemcitabine Action Pathway;Gemcitabine Metabolism Pathway;Purine metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Pyrimidine metabolism;Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.876
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.85

Haploinsufficiency Scores

• pHI: 0.0673
• hipred: N
• hipred_score: 0.154
• ghis: 0.411

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc28a1

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;pyrimidine nucleobase transport;nucleoside transport;pyrimidine-containing compound transmembrane transport;nucleoside transmembrane transport;purine nucleobase transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: nucleoside transmembrane transporter activity;nucleoside:sodium symporter activity;pyrimidine- and adenine-specific:sodium symporter activity