SLC23A1

solute carrier family 23 member 1, the group of Solute carrier family 23

Basic information

Region (hg38): 5:139367195-139384553

Previous symbols: [ "SLC23A2" ]

Links

ENSG00000170482 ∙ NCBI:9963 ∙ OMIM:603790 ∙ HGNC:10974 ∙ Uniprot:Q9UHI7 ∙ 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 SLC23A1 gene.

• Inborn genetic diseases (19 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC23A1 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	2	3
missense			15	3	2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	16	4	5

Variants in SLC23A1

This is a list of pathogenic ClinVar variants found in the SLC23A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-139368787-G-A		not specified	Uncertain significance (Dec 03, 2021)
5-139372053-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-139372062-T-C		not specified	Likely benign (Nov 10, 2022)
5-139372154-A-G		not specified	Uncertain significance (Mar 01, 2023)
5-139372193-A-G		not specified	Likely benign (Jul 06, 2021)
5-139372262-G-A			Benign (Jul 23, 2018)
5-139378010-T-C		not specified	Uncertain significance (Dec 13, 2022)
5-139378019-G-A		not specified	Uncertain significance (Jan 23, 2023)
5-139378082-A-C		not specified	Uncertain significance (Dec 18, 2023)
5-139378291-C-T		not specified	Uncertain significance (Aug 13, 2021)
5-139378327-A-C		not specified	Uncertain significance (May 03, 2023)
5-139378681-G-C			Benign (Apr 11, 2018)
5-139379229-G-T		not specified	Uncertain significance (Dec 21, 2021)
5-139379336-G-A		not specified	Uncertain significance (May 08, 2023)
5-139379730-A-G			Benign (Jun 19, 2018)
5-139379777-C-T		not specified	Uncertain significance (Apr 12, 2023)
5-139379831-T-C			Benign (Jun 12, 2018)
5-139380281-C-T		not specified	Uncertain significance (Dec 12, 2023)
5-139380297-G-C			Likely benign (Nov 01, 2023)
5-139380362-C-T		not specified	Likely benign (Nov 15, 2021)
5-139380557-A-C		not specified	Uncertain significance (Dec 22, 2023)
5-139380843-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-139380881-G-A		not specified	Uncertain significance (Jun 07, 2023)
5-139381938-T-C		not specified	Uncertain significance (Apr 24, 2023)
5-139381950-C-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC23A1	protein_coding	protein_coding	ENST00000353963	14	17358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0235	0.976	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	254	360	0.705	0.0000209	3848
Missense in Polyphen		61	104.72	0.5825		1073
Synonymous	1.71	126	153	0.824	0.0000102	1275
Loss of Function	3.37	8	26.9	0.298	0.00000133	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000273
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000813	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
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 digestion and absorption - Homo sapiens (human);Vitamin C (ascorbate) metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Linoleate metabolism (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.549
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc23a1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); digestive/alimentary phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;sodium ion transport;brain development;response to toxic substance;nucleobase transport;L-ascorbic acid transmembrane transport;L-ascorbic acid metabolic process;sodium ion transmembrane transport;dehydroascorbic acid transport;transepithelial L-ascorbic acid transport
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;basal plasma membrane;membrane;apical plasma membrane;intracellular organelle;extracellular exosome
• Molecular function: transporter activity;protein binding;L-ascorbate:sodium symporter activity;sodium ion transmembrane transporter activity;nucleobase transmembrane transporter activity;L-ascorbic acid transmembrane transporter activity;dehydroascorbic acid transmembrane transporter activity;sodium-dependent L-ascorbate transmembrane transporter activity