SLC23A3

protein-coding

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

Gene summary

Predicted to enable transmembrane transporter activity. Involved in hypoxanthine transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001144889.2

Inheritance

—

ClinVar variants

U:69B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr2:219,161,465-219,170,095

External References & Databases

Ensembl (ENSG00000213901)

Transcript & Mutation Effects

hg38 • Region Span ~8.6 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 SLC23A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144889.2. 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			1 clinvar	2 clinvar		3
missense			66 clinvar	3 clinvar	1 clinvar	70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	69	5	1	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144889.2	RefSeq	NP_001138361.1	12	MANE Select
ENST00000409878.8	Ensembl	ENSP00000386473.4	12	MANE Select
NM_001144890.2	RefSeq	NP_001138362.1	12	Standard
NM_144712.5	RefSeq	NP_653313.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transmembrane transport

Molecular Function

transporter activity
transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000455516
Coding exons: 12
Length: 95499
Individuals with no LoFs: 124774
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 124797
p: 0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	267	322	0.829	0.0000158	3880
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00032	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.666
RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.364

Gene Damage Prediction

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