SLC23A2

protein-coding

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

Gene summary

The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two required transporters and the encoded protein accounts for tissue-specific uptake of vitamin C. Previously, this gene had an official symbol of SLC23A1. [provided by RefSeq, Jul 2008]

Previous symbols:

SLC23A1

MANE transcript

NM_005116.6

Inheritance

—

ClinVar variants

U:56B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr20:4,852,356-5,010,293

External References & Databases

Ensembl (ENSG00000089057)

Transcript & Mutation Effects

hg38 • Region Span ~157.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC23A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005116.6. 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			2 clinvar	1 clinvar	5 clinvar	8
missense			48 clinvar	1 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	56	2	5	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005116.6	RefSeq	NP_005107.4	15	MANE Select
ENST00000338244.6	Ensembl	ENSP00000344322.1	15	MANE Select
NM_203327.2	RefSeq	NP_976072.1	15	Standard
ENST00000379333.5	Ensembl	ENSP00000368637.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin C (ascorbate) metabolism
Metabolism
Metabolism of water-soluble vitamins and cofactors
Metabolism of vitamins and cofactors
Linoleate metabolism

Biological Process

nucleobase-containing compound metabolic process
sodium ion transport
nucleobase transport
L-ascorbic acid transmembrane transport
L-ascorbic acid metabolic process

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

Cellular Component

cytoplasm
plasma membrane
integral component of plasma membrane
basal plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379333
Coding exons: 15
Length: 157938
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.63	190	393	0.484	0.0000230	4203
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na(+) for each ascorbate.;

Recessive Scores

pRec: 0.163

Intolerance Scores

LoFtool: 0.293
RVIS EVS: -0.93
RVIS percentile EVS: 9.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.254

Gene Damage Prediction

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