SLC23A3

solute carrier family 23 member 3, the group of Solute carrier family 23

Basic information

Region (hg38): 2:219161465-219170095

Links

ENSG00000213901 ∙ NCBI:151295 ∙ ∙ HGNC:20601 ∙ Uniprot:Q6PIS1 ∙ 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 SLC23A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC23A3 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			31	2	1	34
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	32	2	1

Variants in SLC23A3

This is a list of pathogenic ClinVar variants found in the SLC23A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219161944-C-G		not specified	Uncertain significance (Mar 16, 2024)
2-219162067-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-219162136-G-A		not specified	Uncertain significance (Sep 30, 2024)
2-219162141-C-T		not specified	Uncertain significance (Jan 27, 2025)
2-219162163-G-A		not specified	Uncertain significance (Oct 02, 2023)
2-219162189-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-219162329-A-G		not specified	Uncertain significance (Aug 05, 2023)
2-219163462-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-219163474-C-T		not specified	Uncertain significance (Oct 25, 2024)
2-219163486-A-G		not specified	Uncertain significance (Jan 04, 2022)
2-219163490-C-T		not specified	Uncertain significance (Jul 30, 2024)
2-219163555-C-T		not specified	Uncertain significance (Feb 25, 2025)
2-219164236-C-A		not specified	Uncertain significance (Nov 09, 2024)
2-219164296-C-T		not specified	Likely benign (Oct 04, 2022)
2-219165179-C-A		not specified	Uncertain significance (Nov 10, 2024)
2-219165194-T-G		not specified	Uncertain significance (Jul 06, 2021)
2-219165294-G-A		not specified	Uncertain significance (Nov 12, 2024)
2-219165296-G-C		not specified	Uncertain significance (Dec 02, 2022)
2-219165371-G-C		not specified	Uncertain significance (Mar 06, 2025)
2-219165389-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-219167966-G-A		not specified	Uncertain significance (Jul 05, 2024)
2-219167995-A-C		not specified	Uncertain significance (Jan 07, 2025)
2-219168016-A-G		not specified	Uncertain significance (Jun 02, 2023)
2-219168196-G-A		not specified	Uncertain significance (Mar 03, 2025)
2-219168205-C-T		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC23A3	protein_coding	protein_coding	ENST00000455516	12	95499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.36e-7	0.995	124774	0	23	124797	0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	267	322	0.829	0.0000158	3880
Missense in Polyphen		65	114.85	0.56598		1420
Synonymous	0.327	132	137	0.964	0.00000661	1407
Loss of Function	2.53	15	29.9	0.501	0.00000184	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000441	0.000439
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.666
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.0822
• hipred: N
• hipred_score: 0.328
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc23a3

Gene ontology

• Biological process: transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: transporter activity;transmembrane transporter activity