SLC28A2

solute carrier family 28 member 2, the group of Solute carrier family 28

Basic information

Region (hg38): 15:45252233-45277846

Links

ENSG00000137860 ∙ NCBI:9153 ∙ OMIM:606208 ∙ HGNC:11002 ∙ Uniprot:O43868 ∙ 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 SLC28A2 gene.

• Inborn genetic diseases (25 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC28A2 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						0
missense			25		2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	2

Variants in SLC28A2

This is a list of pathogenic ClinVar variants found in the SLC28A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-45253253-C-G		not specified	Uncertain significance (Jul 20, 2021)
15-45253255-A-G		not specified	Uncertain significance (Mar 23, 2023)
15-45253280-C-T			Benign (Jan 18, 2019)
15-45253292-T-C		not specified	Uncertain significance (Apr 25, 2023)
15-45253476-A-C		not specified	Uncertain significance (Dec 13, 2022)
15-45253477-G-C		not specified	Uncertain significance (Aug 10, 2023)
15-45253517-A-G		not specified	Uncertain significance (Jul 20, 2021)
15-45262058-A-G		not specified	Uncertain significance (Feb 15, 2023)
15-45262069-C-A			Benign (Jan 18, 2019)
15-45263070-C-T		not specified	Uncertain significance (Nov 17, 2023)
15-45263121-T-C		not specified	Uncertain significance (May 31, 2023)
15-45263232-T-C		not specified	Uncertain significance (Oct 06, 2021)
15-45263985-T-A		not specified	Uncertain significance (Sep 26, 2023)
15-45264016-C-A		not specified	Uncertain significance (Feb 14, 2023)
15-45264680-G-A		not specified	Uncertain significance (May 31, 2023)
15-45265113-G-A		not specified	Uncertain significance (Sep 16, 2021)
15-45265143-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-45265611-G-A		not specified	Uncertain significance (Aug 21, 2023)
15-45265652-G-A		not specified	Uncertain significance (Feb 05, 2024)
15-45266153-G-C		not specified	Uncertain significance (Oct 25, 2023)
15-45266153-G-T		not specified	Uncertain significance (Aug 22, 2023)
15-45267516-C-T		not specified	Uncertain significance (Dec 27, 2022)
15-45267531-G-C		not specified	Uncertain significance (Nov 05, 2021)
15-45267694-C-T		not specified	Uncertain significance (Feb 06, 2023)
15-45267699-A-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC28A2	protein_coding	protein_coding	ENST00000347644	17	23722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-27	0.0000172	125402	1	345	125748	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0913	349	354	0.986	0.0000176	4273
Missense in Polyphen		121	125.6	0.96341		1639
Synonymous	0.0543	135	136	0.994	0.00000723	1324
Loss of Function	-0.889	38	32.5	1.17	0.00000138	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00652	0.00649
Finnish	0.000924	0.000924
European (Non-Finnish)	0.00130	0.00130
Middle Eastern	0.00652	0.00649
South Asian	0.000787	0.000784
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent and purine-selective transporter. Exhibits the transport characteristics of the nucleoside transport system cif or N1 subtype (N1/cif) (selective for purine nucleosides and uridine). Plays a critical role in specific uptake and salvage of purine nucleosides in kidney and other tissues.
• Pathway: Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Mercaptopurine 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: 0.151

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.31

Haploinsufficiency Scores

• pHI: 0.0450
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc28a2

Gene ontology

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