SLC39A11

protein-coding

solute carrier family 39 member 11, the group of Solute carrier family 39

Gene summary

Predicted to enable copper ion transmembrane transporter activity and zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C17orf26

MANE transcript

NM_139177.4

Inheritance

—

ClinVar variants

U:65B:8

Top phenotype

Ependymoma

gnomAD constraint

pLI —, LoF o/e 1.42

Max pathogenic AF

—

Genomic locus

chr17:72,645,949-73,092,712

External References & Databases

Ensembl (ENSG00000133195)

Transcript & Mutation Effects

hg38 • Region Span ~446.8 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 SLC39A11 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 5

EpendymomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139177.4. 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 clinvar	1 clinvar	5
missense			55 clinvar	4 clinvar	1 clinvar	60
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	65	6	2	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 91 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139177.4	RefSeq	NP_631916.2	9	MANE Select
ENST00000255559.8	Ensembl	ENSP00000255559.3	9	MANE Select
NM_001159770.2	RefSeq	NP_001153242.1	9	Standard
NM_001352691.2	RefSeq	NP_001339620.1	9	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 transmembrane transport

Molecular Function

zinc ion transmembrane transporter activity

Cellular Component

fungal-type vacuole membrane
nucleus
cytoplasm
Golgi apparatus
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000542342
Coding exons: 9
Length: 446764
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 125748
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.127	206	201	1.03	0.0000112	2178
Missense (PolyPhen)		94	95.626	0.983		1011
Synonymous	-0.405	91	86.2	1.06	0.00000584	740
Loss of Function	-1.55	23	16.3	1.42	8.39e-7	172

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a cellular zinc transporter. {ECO:0000250|UniProtKB:Q8BWY7}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.860
RVIS EVS: 0.64
RVIS percentile EVS: 84.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0935

Gene Damage Prediction

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