SLC30A8

solute carrier family 30 member 8, the group of Solute carrier family 30

Basic information

Region (hg38): 8:116950273-117176714

Links

ENSG00000164756 ∙ NCBI:169026 ∙ OMIM:611145 ∙ HGNC:20303 ∙ Uniprot:Q8IWU4 ∙ 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 SLC30A8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A8 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				4		4
missense			16	2	3	21
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	18	6	3

Variants in SLC30A8

This is a list of pathogenic ClinVar variants found in the SLC30A8 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-117135391-C-T		SLC30A8-related disorder	Likely benign (Jun 18, 2019)
8-117146954-T-C			Benign (Feb 08, 2018)
8-117146981-TAAAGATC-T		Type 2 diabetes mellitus	protective (Apr 01, 2014)
8-117146991-T-C		not specified	Uncertain significance (Oct 03, 2023)
8-117147014-G-T		not specified	Uncertain significance (Apr 19, 2024)
8-117147015-C-A		not specified	Uncertain significance (Nov 15, 2021)
8-117147042-C-T		not specified	Uncertain significance (Jun 10, 2024)
8-117147054-A-C		not specified	Likely benign (May 27, 2022)
8-117147084-G-A		not specified	Uncertain significance (Jun 22, 2024)
8-117147117-G-A		not specified	Uncertain significance (Dec 07, 2021)
8-117147149-C-T			Likely benign (Apr 03, 2018)
8-117152949-C-T		not specified	Uncertain significance (Jun 11, 2024)
8-117153064-G-A		not specified	Uncertain significance (Jan 03, 2024)
8-117153084-C-T		Type 2 diabetes mellitus	protective (Apr 01, 2014)
8-117157765-C-T		SLC30A8-related disorder	Benign (Aug 13, 2019)
8-117157774-T-C		not specified	Likely benign (May 05, 2023)
8-117157816-T-C		not specified	Uncertain significance (Aug 17, 2021)
8-117161757-C-T		Type 2 diabetes mellitus	Uncertain significance (Mar 17, 2024)
8-117161787-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-117161797-A-G		not specified	Uncertain significance (Oct 12, 2022)
8-117161811-G-A		not specified	Uncertain significance (Dec 07, 2021)
8-117161837-T-C			Likely benign (Sep 11, 2018)
8-117161879-C-G		not specified	Uncertain significance (Mar 08, 2024)
8-117163447-C-T		not specified	Uncertain significance (Apr 26, 2023)
8-117163456-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A8	protein_coding	protein_coding	ENST00000456015	8	226442

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.43e-12	0.0373	125557	0	191	125748	0.000760

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.109	200	204	0.979	0.0000105	2414
Missense in Polyphen		64	66.457	0.96303		835
Synonymous	0.907	72	82.5	0.873	0.00000474	727
Loss of Function	-0.0479	17	16.8	1.01	7.89e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00186	0.00185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000472	0.000466
Middle Eastern	0.000163	0.000163
South Asian	0.00284	0.00281
Other	0.000825	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitates the accumulation of zinc from the cytoplasm into intracellular vesicles, being a zinc-efflux transporter. May be a major component for providing zinc to insulin maturation and/or storage processes in insulin-secreting pancreatic beta- cells. {ECO:0000269|PubMed:16984975}.
• Pathway: Zinc homeostasis;Peptide hormone metabolism;Metabolism of proteins;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Insulin processing;Metal ion SLC transporters;Zinc efflux and compartmentalization by the SLC30 family;Zinc transporters (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.998
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.229

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a8
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: slc30a8
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: zinc ion transport;cellular zinc ion homeostasis;response to glucose;response to zinc ion;insulin secretion;positive regulation of insulin secretion;sequestering of zinc ion;response to interferon-gamma;glucose homeostasis;regulation of vesicle-mediated transport;regulation of sequestering of zinc ion;response to interleukin-1;zinc ion transmembrane transport
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;secretory granule;transport vesicle membrane;secretory granule membrane;cytoplasmic vesicle
• Molecular function: zinc ion transmembrane transporter activity;protein binding;zinc ion binding;protein homodimerization activity