SLC23A2

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

Basic information

Region (hg38): 20:4852355-5010293

Previous symbols: [ "SLC23A1" ]

Links

ENSG00000089057 ∙ NCBI:9962 ∙ OMIM:603791 ∙ HGNC:10973 ∙ Uniprot:Q9UGH3 ∙ 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 SLC23A2 gene.

• Inborn genetic diseases (14 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.

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				1	5	6
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	2	6

Variants in SLC23A2

This is a list of pathogenic ClinVar variants found in the SLC23A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-4856979-G-A		not specified	Uncertain significance (Mar 21, 2023)
20-4857126-G-A		not specified	Uncertain significance (Aug 16, 2022)
20-4857171-T-C		not specified	Uncertain significance (Dec 22, 2023)
20-4857181-G-A		not specified	Uncertain significance (Sep 22, 2023)
20-4867829-C-A		not specified	Uncertain significance (Jun 22, 2023)
20-4869923-G-T			Likely benign (Jun 23, 2018)
20-4869998-G-A			Benign (Jan 03, 2019)
20-4873958-C-A			Benign (Jul 23, 2018)
20-4874607-G-A		not specified	Uncertain significance (Apr 25, 2023)
20-4874663-G-A			Benign (Dec 31, 2019)
20-4883652-T-C		not specified	Uncertain significance (Dec 03, 2021)
20-4883680-C-T			Benign (Jul 23, 2018)
20-4884757-C-T		not specified	Uncertain significance (Jul 11, 2023)
20-4884776-T-A		not specified	Uncertain significance (Jun 28, 2022)
20-4885830-T-C		not specified	Uncertain significance (Oct 12, 2022)
20-4899545-C-T			Benign (Mar 31, 2018)
20-4902489-T-C		not specified	Uncertain significance (May 11, 2022)
20-4902509-C-T		not specified	Uncertain significance (Nov 21, 2022)
20-4902521-A-G		not specified	Uncertain significance (Jun 24, 2022)
20-4902554-G-A		not specified	Uncertain significance (May 27, 2022)
20-4912894-C-T		not specified	Uncertain significance (May 27, 2022)
20-4912902-G-A		not specified	Uncertain significance (Mar 07, 2024)
20-4912913-C-T			Benign (Aug 16, 2018)
20-4912948-C-T			Likely benign (Jun 14, 2018)
20-4912950-C-T		not specified	Uncertain significance (Apr 11, 2023)

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
0.00626	0.994	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

Haploinsufficiency Scores

• pHI: 0.504
• hipred: Y
• hipred_score: 0.563
• ghis: 0.590

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

Mouse Genome Informatics

• Gene name: Slc23a2
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

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