SLC28A3

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

Basic information

Region (hg38): 9:84275456-84340758

Links

ENSG00000197506 ∙ NCBI:64078 ∙ OMIM:608269 ∙ HGNC:16484 ∙ Uniprot:Q9HAS3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC28A3 gene.

• Inborn genetic diseases (19 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC28A3 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					3	3
missense			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	4

Variants in SLC28A3

This is a list of pathogenic ClinVar variants found in the SLC28A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-84280005-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-84280050-G-A		not specified	Uncertain significance (Jan 04, 2022)
9-84280878-C-T		not specified	Uncertain significance (Sep 13, 2023)
9-84285365-C-G		not specified	Uncertain significance (Mar 07, 2023)
9-84285439-T-C		not specified	Uncertain significance (Apr 25, 2023)
9-84285536-A-G		not specified	Uncertain significance (Sep 17, 2021)
9-84285993-C-G		not specified	Uncertain significance (Feb 15, 2023)
9-84286011-G-A			Benign (Jul 15, 2019)
9-84288152-C-T			Benign (May 09, 2018)
9-84288172-A-G		not specified	Uncertain significance (Jun 13, 2023)
9-84290181-G-A			Benign (May 09, 2018)
9-84290203-C-G		not specified	Uncertain significance (Jul 05, 2023)
9-84290212-A-C		not specified	Uncertain significance (Jan 23, 2023)
9-84290222-G-A		not specified	Uncertain significance (Oct 25, 2023)
9-84290225-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-84290260-A-G		not specified	Uncertain significance (Mar 31, 2023)
9-84292742-A-G		not specified	Uncertain significance (Oct 17, 2023)
9-84294268-G-A		not specified	Uncertain significance (Jan 26, 2023)
9-84297998-A-G		not specified	Uncertain significance (Mar 07, 2024)
9-84299626-T-C		not specified	Uncertain significance (May 23, 2023)
9-84299682-C-G		not specified	Uncertain significance (Sep 26, 2023)
9-84299713-G-C		not specified	Uncertain significance (Jan 23, 2024)
9-84302216-A-C		not specified	Uncertain significance (Oct 13, 2023)
9-84302281-A-T		not specified	Uncertain significance (Oct 20, 2023)
9-84302284-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC28A3	protein_coding	protein_coding	ENST00000376238	18	65301

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-23	0.00175	125533	0	215	125748	0.000855

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	321	379	0.846	0.0000195	4514
Missense in Polyphen		98	126.7	0.77347		1551
Synonymous	0.643	134	144	0.932	0.00000844	1336
Loss of Function	0.340	36	38.3	0.941	0.00000178	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00176	0.00175
Ashkenazi Jewish	0.00	0.00
East Asian	0.00466	0.00458
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000459	0.000457
Middle Eastern	0.00466	0.00458
South Asian	0.00102	0.00101
Other	0.000332	0.000326

dbNSFP

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}.
• Pathway: Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Gemcitabine Action Pathway;Mercaptopurine Metabolism 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: 0.117

Intolerance Scores

• loftool: 0.964
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.161
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0800

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc28a3

Gene ontology

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