SLC30A6

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

Basic information

Region (hg38): 2:32165841-32224379

Links

ENSG00000152683 ∙ NCBI:55676 ∙ OMIM:611148 ∙ HGNC:19305 ∙ Uniprot:Q6NXT4 ∙ 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 SLC30A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A6 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						0
missense			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in SLC30A6

This is a list of pathogenic ClinVar variants found in the SLC30A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-32171341-C-T		not specified	Uncertain significance (Aug 12, 2022)
2-32171369-G-A		not specified	Uncertain significance (Apr 25, 2023)
2-32174102-T-C		not specified	Uncertain significance (Feb 26, 2025)
2-32174130-G-A		not specified	Uncertain significance (Apr 26, 2024)
2-32174138-A-G		not specified	Uncertain significance (Dec 21, 2023)
2-32175357-T-C		not specified	Uncertain significance (Jun 25, 2024)
2-32184322-C-T		not specified	Uncertain significance (May 23, 2023)
2-32184328-T-C		not specified	Uncertain significance (Jan 26, 2023)
2-32192949-C-T		not specified	Uncertain significance (Nov 30, 2021)
2-32193909-C-T		not specified	Uncertain significance (Aug 14, 2024)
2-32193912-T-C		not specified	Uncertain significance (Dec 16, 2023)
2-32193935-T-C		not specified	Uncertain significance (Feb 11, 2025)
2-32193939-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-32193948-C-A		not specified	Uncertain significance (Apr 19, 2024)
2-32193953-C-T		not specified	Uncertain significance (May 13, 2024)
2-32197352-A-G		not specified	Uncertain significance (Sep 15, 2021)
2-32197743-C-A		not specified	Uncertain significance (Sep 01, 2021)
2-32197751-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-32197772-T-C		not specified	Uncertain significance (Jan 02, 2024)
2-32197786-G-A		not specified	Uncertain significance (May 29, 2024)
2-32197795-C-G		not specified	Uncertain significance (Feb 26, 2025)
2-32197799-G-T		not specified	Uncertain significance (Nov 16, 2022)
2-32204603-G-A		not specified	Uncertain significance (Apr 18, 2023)
2-32204660-A-G		not specified	Uncertain significance (Jan 26, 2025)
2-32204686-A-C		not specified	Uncertain significance (Jan 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A6	protein_coding	protein_coding	ENST00000379343	15	58516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.91e-9	0.970	125709	0	34	125743	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0266	248	249	0.995	0.0000123	3242
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000390	0.000390
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.000133	0.000131
Other	0.000165	0.000163

dbNSFP

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}.
• 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: 0.0997

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.446
• hipred: N
• hipred_score: 0.426
• ghis: 0.685

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a6

Gene ontology

• Biological process: zinc ion transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: zinc ion transmembrane transporter activity