SLC30A4

solute carrier family 30 member 4, the group of Solute carrier family 30

Basic information

Region (hg38): 15:45479606-45522755

Previous symbols: [ "ZNT4" ]

Links

ENSG00000104154

∙ NCBI:7782 ∙ OMIM:602095 ∙ HGNC:11015 ∙ Uniprot:O14863 ∙ 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 SLC30A4 gene.

not_specified (42 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013309.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			39 clinvar	3 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A4	protein_coding	protein_coding	ENST00000261867	7	43197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.115	0.883	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	190	235	0.807	0.0000111	2799
Missense in Polyphen		50	81.777	0.61142		1031
Synonymous	1.19	75	89.3	0.840	0.00000429	847
Loss of Function	2.86	5	18.2	0.275	9.32e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probably involved in zinc transport out of the cytoplasm, maybe by sequestration into an intracellular compartment.;
Pathway: Zinc homeostasis (Consensus)

Recessive Scores

pRec: 0.125

Intolerance Scores

loftool: 0.0898
rvis_EVS: -0.52
rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

pHI: 0.0849
hipred: Y
hipred_score: 0.699
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.00295

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc30a4
Phenotype: pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; hearing/vestibular/ear phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process: response to toxic substance;response to zinc ion;zinc ion homeostasis;regulation of sequestering of zinc ion;zinc ion transmembrane transport
Cellular component: cytoplasm;lysosomal membrane;late endosome;plasma membrane;integral component of membrane;late endosome membrane
Molecular function: zinc ion transmembrane transporter activity;protein binding