SLC23A2

solute carrier family 23 member 2, the group of Solute carrier family 23

Basic information

Region (hg38): 20:4852356-5010293

Previous symbols: [ "SLC23A1" ]

Links

ENSG00000089057 ∙ NCBI:9962 ∙ OMIM:603791 ∙ HGNC:10973 ∙ Uniprot:Q9UGH3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 41.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_005116.6	NP_005107.4	15	yes	-
ENST00000338244.6	ENSP00000344322.1	15	yes	-
NM_203327.2	NP_976072.1	15	-	-
ENST00000379333.5	ENSP00000368637.1	15	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC23A2 gene.

• not_specified (45 variants)
• not_provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC23A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_005116.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	1	5	8
missense			48	1		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6			6
Total	0	0	56	2	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC23A2	protein_coding	protein_coding	ENST00000379333	15	157938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.63	190	393	0.484	0.0000230	4203
Missense in Polyphen		68	180.94	0.37581		1976
Synonymous	-1.17	183	164	1.12	0.0000112	1336
Loss of Function	3.61	10	32.1	0.312	0.00000159	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na(+) for each ascorbate.
• Pathway: Vitamin C (ascorbate) metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Linoleate metabolism (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.293
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;sodium ion transport;nucleobase transport;L-ascorbic acid transmembrane transport;L-ascorbic acid metabolic process;transepithelial L-ascorbic acid transport
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;basal plasma membrane;membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane
• Molecular function: transporter activity;L-ascorbate:sodium symporter activity;nucleobase transmembrane transporter activity;L-ascorbic acid transmembrane transporter activity;sodium-dependent L-ascorbate transmembrane transporter activity