SLC30A6

protein-coding

solute carrier family 30 member 6, the group of Solute carrier family 30

Gene summary

This gene encodes a member of a family of proteins that function as zinc transporters. This protein can regulate subcellular levels of zinc in the Golgi and vesicles. Expression of this gene is altered in the Alzheimer's disease brain plaques. [provided by RefSeq, Aug 2016]

MANE transcript

NM_017964.5

Inheritance

—

ClinVar variants

U:67B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr2:32,165,841-32,224,379

External References & Databases

Ensembl (ENSG00000152683)

Transcript & Mutation Effects

hg38 • Region Span ~58.5 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 SLC30A6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 67

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017964.5. 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			63 clinvar	4 clinvar		67
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	67	5	0	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017964.5	RefSeq	NP_060434.2	14	MANE Select
ENST00000282587.9	Ensembl	ENSP00000282587.5	14	MANE Select
NM_001193513.3	RefSeq	NP_001180442.1	15	Standard
NM_001193514.3	RefSeq	NP_001180443.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Zinc homeostasis
Peptide hormone metabolism
Metabolism of proteins
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport

Biological Process

zinc ion transmembrane transport

Molecular Function

zinc ion transmembrane transporter activity

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379343
Coding exons: 15
Length: 58516
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125743
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0266	248	249	0.995	0.0000123	3242
Missense (PolyPhen)		42	54.524	0.7703		721
Synonymous	-2.09	110	85.4	1.29	0.00000417	986
Loss of Function	2.13	18	30.8	0.585	0.00000195	342

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00027	0.00027	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Zinc-efflux transporter which allocates the cytoplasmic zinc to the trans-Golgi network (TGN) as well as the vesicular compartment. {ECO:0000250}.;

Recessive Scores

pRec: 0.0997

Intolerance Scores

LoFtool: 0.275
RVIS EVS: -1
RVIS percentile EVS: 8.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.277

Gene Damage Prediction

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