SLC39A12

protein-coding

solute carrier family 39 member 12, the group of Solute carrier family 39

Gene summary

Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]

MANE transcript

NM_001145195.2

Inheritance

ClinVar variants

U:96B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr10:17,951,839-18,043,292

External References & Databases

Ensembl (ENSG00000148482)

Transcript & Mutation Effects

hg38 • Region Span ~91.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC39A12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145195.2. 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			95 clinvar	5 clinvar	1 clinvar	101
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	6	1	103

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145195.2	RefSeq	NP_001138667.1	12	MANE Select
ENST00000377369.7	Ensembl	ENSP00000366586.2	12	MANE Select
NM_001282733.2	RefSeq	NP_001269662.1	12	Standard
NM_001282734.2	RefSeq	NP_001269663.1	11	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

cellular zinc ion homeostasis
signal transduction
regulation of neuron projection development
regulation of microtubule polymerization
zinc ion import across plasma membrane

Molecular Function

zinc ion transmembrane transporter activity

Cellular Component

integral component of plasma membrane
perinuclear region of cytoplasm
extracellular vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377369
Coding exons: 12
Length: 91454
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125748
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.285	375	360	1.04	0.0000177	4522
Missense (PolyPhen)		103	117.13	0.87936		1517
Synonymous	-0.393	145	139	1.04	0.00000719	1346
Loss of Function	2.57	15	30.3	0.495	0.00000135	390

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00076	0.00076	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a zinc-influx transporter (Potential). May be partly involved in the outbreak of schizophrenia. {ECO:0000305}.;

Recessive Scores

pRec: 0.0921

Intolerance Scores

LoFtool: 0.865
RVIS EVS: 0.71
RVIS percentile EVS: 85.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.164

Gene Damage Prediction

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