SLC39A9

protein-coding

solute carrier family 39 member 9, the group of Solute carrier family 39

Gene summary

Enables G protein-coupled receptor activity; androgen binding activity; and zinc efflux transmembrane transporter activity. Involved in intracellular zinc ion homeostasis; regulation of vascular endothelial cell proliferation; and zinc ion transmembrane transport. Located in several cellular components, including mitochondrial membrane; perinuclear region of cytoplasm; and trans-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018375.5

Inheritance

—

ClinVar variants

U:29B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr14:69,398,015-69,462,390

External References & Databases

Ensembl (ENSG00000029364)

Transcript & Mutation Effects

hg38 • Region Span ~64.4 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 SLC39A9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018375.5. 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	1
missense			29 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	0	1	30

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018375.5	RefSeq	NP_060845.2	7	MANE Select
ENST00000336643.10	Ensembl	ENSP00000336887.5	7	MANE Select
NM_001252148.2	RefSeq	NP_001239077.1	6	Standard
NM_001252150.2	RefSeq	NP_001239079.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nuclear Receptors Meta-Pathway
NRF2 pathway
Zinc homeostasis

Biological Process

zinc ion transport
transmembrane transport

Molecular Function

metal ion transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336643
Coding exons: 7
Length: 64374
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125746
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.97	103	177	0.582	0.00000923	1966
Missense (PolyPhen)		34	69.764	0.48736		790
Synonymous	0.710	65	72.7	0.894	0.00000419	676
Loss of Function	2.83	2	13.0	0.154	7.12e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a zinc-influx transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.478
RVIS EVS: 0.19
RVIS percentile EVS: 66.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.589

Gene Damage Prediction

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