SLC30A3

protein-coding

solute carrier family 30 member 3, the group of Solute carrier family 30

Gene summary

Enables zinc ion transmembrane transporter activity. Involved in zinc ion import into lysosome. Located in cytoplasmic vesicle; lysosomal membrane; and microvesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNT3

MANE transcript

NM_003459.5

Inheritance

—

ClinVar variants

U:48B:6

Top phenotype

Febrile seizure (within the age range of 3 months to 6 years)

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr2:27,253,684-27,275,817

External References & Databases

Ensembl (ENSG00000115194)

Transcript & Mutation Effects

hg38 • Region Span ~22.1 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 SLC30A3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 7

Febrile seizure (within the age range of 3 months to 6 years)Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003459.5. 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	3 clinvar	2 clinvar	6
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	4	2	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003459.5	RefSeq	NP_003450.2	8	MANE Select
ENST00000233535.9	Ensembl	ENSP00000233535.4	8	MANE Select
NM_001318949.2	RefSeq	NP_001305878.1	9	Standard
NM_001318950.2	RefSeq	NP_001305879.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Zinc homeostasis
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport
Transport of small molecules
Metal ion SLC transporters

Biological Process

response to zinc ion
positive regulation of transport
regulation of sequestering of zinc ion
zinc ion transmembrane transport
zinc ion import into synaptic vesicle

Molecular Function

zinc ion transmembrane transporter activity
protein binding
zinc-transporting ATPase activity

Cellular Component

cytoplasm
lysosomal membrane
endosome
late endosome
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000233535
Coding exons: 8
Length: 22134
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125745
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.73	170	247	0.689	0.0000151	2453
Missense (PolyPhen)		38	74.502	0.51005		753
Synonymous	0.314	104	108	0.962	0.00000685	853
Loss of Function	2.90	3	15.2	0.197	7.98e-7	168

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in accumulation of zinc in synaptic vesicles. {ECO:0000250|UniProtKB:P97441}.;

Recessive Scores

pRec: 0.159

Intolerance Scores

LoFtool: 0.499
RVIS EVS: -0.8
RVIS percentile EVS: 12.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.881

Gene Damage Prediction

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