SLC30A3

solute carrier family 30 member 3, the group of Solute carrier family 30

Basic information

Region (hg38): 2:27253683-27275817

Previous symbols: [ "ZNT3" ]

Links

ENSG00000115194 ∙ NCBI:7781 ∙ OMIM:602878 ∙ HGNC:11014 ∙ Uniprot:Q99726 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC30A3 gene.

• Inborn genetic diseases (16 variants)
• not provided (7 variants)
• Febrile seizure (within the age range of 3 months to 6 years) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	15	5	1

Variants in SLC30A3

This is a list of pathogenic ClinVar variants found in the SLC30A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-27255323-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-27255325-G-C		Febrile seizure (within the age range of 3 months to 6 years) • not specified	Uncertain significance (Dec 21, 2022)
2-27255334-C-T		not specified	Uncertain significance (Nov 22, 2022)
2-27255352-A-G		not specified	Uncertain significance (Dec 22, 2023)
2-27255359-G-A		not specified	Uncertain significance (Feb 26, 2024)
2-27256387-G-T			Benign (Dec 14, 2018)
2-27256412-T-A		not specified	Uncertain significance (Dec 21, 2023)
2-27256446-C-T		not specified	Uncertain significance (Nov 18, 2023)
2-27256458-G-A		not specified	Uncertain significance (Aug 11, 2022)
2-27256467-G-A		not specified	Uncertain significance (Nov 13, 2023)
2-27256471-C-T			Likely benign (Feb 25, 2018)
2-27256487-C-T		not specified	Uncertain significance (Nov 01, 2022)
2-27257168-G-A		not specified	Uncertain significance (Feb 21, 2024)
2-27257237-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-27257299-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-27257318-G-C		not specified	Uncertain significance (Jun 06, 2023)
2-27257318-G-T		not specified	Uncertain significance (Dec 06, 2021)
2-27257323-G-T		not specified	Uncertain significance (Sep 17, 2021)
2-27257910-G-A			Likely benign (Dec 14, 2017)
2-27257983-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-27258027-G-A			Likely benign (May 17, 2018)
2-27258040-G-A		not specified	Uncertain significance (Aug 08, 2023)
2-27258067-G-T			Likely benign (Jun 26, 2018)
2-27258239-T-A		not specified	Uncertain significance (Jun 24, 2022)
2-27258793-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A3	protein_coding	protein_coding	ENST00000233535	8	22134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.542	0.457	125735	0	10	125745	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	170	247	0.689	0.0000151	2453
Missense in Polyphen		38	74.502	0.51005		753
Synonymous	0.314	104	108	0.962	0.00000685	853
Loss of Function	2.90	3	15.2	0.197	7.98e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.00000894	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in accumulation of zinc in synaptic vesicles. {ECO:0000250|UniProtKB:P97441}.
• Pathway: Zinc homeostasis;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc efflux and compartmentalization by the SLC30 family;Zinc transporters (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.499
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.408
• hipred: Y
• hipred_score: 0.789
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a3
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: response to zinc ion;positive regulation of transport;regulation of sequestering of zinc ion;zinc ion transmembrane transport;zinc ion import into synaptic vesicle
• Cellular component: cytoplasm;lysosomal membrane;endosome;late endosome;plasma membrane;integral component of plasma membrane;synaptic vesicle;membrane;cell junction;integral component of synaptic vesicle membrane;late endosome membrane;neuron projection;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse
• Molecular function: zinc ion transmembrane transporter activity;protein binding;zinc-transporting ATPase activity