SLC30A1

protein-coding

solute carrier family 30 member 1, the group of Solute carrier family 30

Gene summary

Enables calcium:monoatomic cation antiporter activity and zinc:proton antiporter activity. Involved in defense response to bacterium; intracellular zinc ion homeostasis; and transition metal ion transport. Located in several cellular components, including Golgi apparatus; basolateral plasma membrane; and nuclear membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNT1

MANE transcript

NM_021194.3

Inheritance

—

ClinVar variants

U:33

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:211,571,568-211,579,161

External References & Databases

Ensembl (ENSG00000170385)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 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 SLC30A1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021194.3. 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						0
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	0	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021194.3	RefSeq	NP_067017.2	2	MANE Select
ENST00000367001.5	Ensembl	ENSP00000355968.4	2	MANE Select
ENST00001123489.1	Ensembl	ENSP00000793294.1	2	Standard
ENST00001143740.1	Ensembl	ENSP00000809157.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mineral absorption - Homo sapiens (human)
Zinc homeostasis
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

in utero embryonic development
zinc ion transport
cellular calcium ion homeostasis
cellular zinc ion homeostasis
negative regulation of neurotransmitter secretion

Molecular Function

zinc ion transmembrane transporter activity
protein binding
calcium channel inhibitor activity

Cellular Component

cytoplasm
endoplasmic reticulum
Golgi apparatus
plasma membrane
T-tubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367001
Coding exons: 2
Length: 7175
Individuals with no LoFs: 122679
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 122680
p: 0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.20	183	288	0.635	0.0000132	3306
Missense (PolyPhen)		31	106.05	0.29231		1204
Synonymous	0.653	105	114	0.922	0.00000553	1056
Loss of Function	3.32	0	12.8	0.00	6.09e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in zinc transport out of the cell.;

Recessive Scores

pRec: 0.210

Intolerance Scores

RVIS EVS: -0.38
RVIS percentile EVS: 27.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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