SLC30A4

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

Basic information

Region (hg38): 15:45479605-45522755

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.

• Inborn genetic diseases (17 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.

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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in SLC30A4

This is a list of pathogenic ClinVar variants found in the SLC30A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-45485233-G-C		not specified	Uncertain significance (Aug 12, 2021)
15-45485251-A-T		not specified	Uncertain significance (Jul 06, 2021)
15-45485271-G-T		not specified	Likely benign (May 10, 2022)
15-45487542-C-T		not specified	Uncertain significance (Jun 17, 2022)
15-45488960-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-45488965-C-A		not specified	Uncertain significance (Jan 26, 2022)
15-45488981-T-G		not specified	Uncertain significance (Feb 15, 2023)
15-45489011-G-A		not specified	Uncertain significance (Mar 23, 2023)
15-45489016-C-A		not specified	Uncertain significance (Sep 27, 2021)
15-45490812-A-G		not specified	Uncertain significance (Apr 05, 2023)
15-45490822-A-T		not specified	Uncertain significance (Aug 17, 2021)
15-45522045-T-A		not specified	Likely benign (Dec 17, 2023)
15-45522062-C-T		not specified	Uncertain significance (Dec 11, 2023)
15-45522065-T-C		not specified	Uncertain significance (Apr 26, 2023)
15-45522097-A-C		not specified	Uncertain significance (Jun 16, 2023)
15-45522098-C-T		not specified	Uncertain significance (Dec 22, 2023)
15-45522120-G-T		not specified	Uncertain significance (Oct 12, 2022)
15-45522129-A-T		not specified	Uncertain significance (Jun 21, 2021)
15-45522156-G-A		not specified	Uncertain significance (Dec 17, 2023)
15-45522165-C-G		not specified	Uncertain significance (Jun 02, 2023)
15-45522306-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-45522317-A-C		not specified	Uncertain significance (Jul 19, 2023)

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