SLC39A3

protein-coding

solute carrier family 39 member 3, the group of Solute carrier family 39

Gene summary

Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to act upstream of or within several processes, including T cell homeostasis; chordate embryonic development; and zinc ion transport. Predicted to be located in hippocampal mossy fiber to CA3 synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144564.5

Inheritance

—

ClinVar variants

U:71B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr19:2,732,204-2,740,028

External References & Databases

Ensembl (ENSG00000141873)

Transcript & Mutation Effects

hg38 • Region Span ~7.8 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 SLC39A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144564.5. 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						0
missense			71 clinvar	1 clinvar	1 clinvar	73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	1	1	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144564.5	RefSeq	NP_653165.2	2	MANE Select
ENST00000269740.9	Ensembl	ENSP00000269740.3	2	MANE Select
NM_213568.2	RefSeq	NP_998733.1	1	Standard
ENST00000455372.2	Ensembl	ENSP00000393715.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nuclear Receptors Meta-Pathway
NRF2 pathway
Zinc homeostasis
Senescence and Autophagy in Cancer
Zinc influx into cells by the SLC39 gene family

Biological Process

cell morphogenesis
in utero embryonic development
T cell homeostasis
embryonic cranial skeleton morphogenesis
limb development

Molecular Function

zinc ion transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269740
Coding exons: 2
Length: 7949
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125720
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.669	189	217	0.872	0.0000154	2005
Missense (PolyPhen)		60	73.328	0.81824		714
Synonymous	-2.40	152	119	1.28	0.00000999	719
Loss of Function	1.34	2	5.33	0.375	2.25e-7	70

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a zinc-influx transporter. {ECO:0000305}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.104
RVIS EVS: -0.02
RVIS percentile EVS: 52.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.497

Gene Damage Prediction

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