SLC43A3

protein-coding

solute carrier family 43 member 3, the group of Solute carrier family 43

Gene summary

Enables adenine transmembrane transporter activity; guanine transmembrane transporter activity; and xenobiotic transmembrane transporter activity. Involved in hypoxanthine transport. Located in basolateral plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_199329.3

Inheritance

—

ClinVar variants

U:77B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr11:57,406,954-57,427,580

External References & Databases

Ensembl (ENSG00000134802)

Transcript & Mutation Effects

hg38 • Region Span ~20.6 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 SLC43A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199329.3. 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			2
missense			67 clinvar	1 clinvar		68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	77	1	0	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 118 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199329.3	RefSeq	NP_955361.1	12	MANE Select
ENST00000395124.6	Ensembl	ENSP00000378556.1	12	MANE Select
NM_001278201.2	RefSeq	NP_001265130.1	12	Standard
NM_001278206.2	RefSeq	NP_001265135.1	12	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
slc43a3a	Danio rerio	Structure: ventricular system Quality: hydrocephalic abnormal

Gene / Model

Organism

Observed Phenotype

slc43a3a

Danio rerio

Structure: ventricular system

Quality: hydrocephalic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
transmembrane transport

Molecular Function

molecular_function

Cellular Component

cellular_component
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395123
Coding exons: 12
Length: 20627
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125748
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.475	260	282	0.920	0.0000157	3172
Missense (PolyPhen)		56	79.906	0.70083		946
Synonymous	0.828	105	116	0.902	0.00000634	1019
Loss of Function	2.10	13	24.1	0.539	0.00000123	257

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00029	0.00029	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.0971

Intolerance Scores

LoFtool: 0.570
RVIS EVS: -0.51
RVIS percentile EVS: 21.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.281

Gene Damage Prediction

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