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.

• not_specified (62 variants)

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. These statistics are base on transcript: NM_000017964.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			57	4		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	5	0

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