SLC30A2

solute carrier family 30 member 2, the group of Solute carrier family 30

Basic information

Region (hg38): 1:26037252-26046118

Previous symbols: [ "ZNT2" ]

Links

ENSG00000158014 ∙ NCBI:7780 ∙ OMIM:609617 ∙ HGNC:11013 ∙ Uniprot:Q9BRI3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Zinc deficiency, transient neonata	AD	Biochemical	Infants born to mothers with causative variants can show signs of zinc deficiency, and awareness may allow zinc supplementation in the infant's diet	Biochemical	17065149; 22733820

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC30A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A2 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				1	1	2
missense			13		1	14
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	1	13	2	2

Variants in SLC30A2

This is a list of pathogenic ClinVar variants found in the SLC30A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26039173-C-T			Uncertain significance (-)
1-26039261-G-C		Inborn genetic diseases	Uncertain significance (May 09, 2023)
1-26039278-A-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
1-26039291-C-T		Inborn genetic diseases	Uncertain significance (May 06, 2022)
1-26039805-C-G		Inborn genetic diseases	Uncertain significance (Feb 03, 2023)
1-26039823-C-G		Inborn genetic diseases	Uncertain significance (Mar 21, 2022)
1-26039829-A-G			Benign (Aug 14, 2018)
1-26039833-A-G		Inborn genetic diseases	Uncertain significance (Apr 26, 2024)
1-26039897-C-T		Inborn genetic diseases	Uncertain significance (Mar 28, 2024)
1-26042626-C-T		Malignant tumor of prostate	Uncertain significance (-)
1-26042629-G-A			Pathogenic (Mar 21, 2024)
1-26042632-C-G		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
1-26042665-C-T		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
1-26042666-G-A		SLC30A2-related disorder	Likely benign (Dec 16, 2019)
1-26042704-C-G		Inborn genetic diseases	Uncertain significance (May 30, 2024)
1-26042708-T-C		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
1-26043441-TC-T		Zinc deficiency, transient neonatal	Likely pathogenic (May 25, 2020)
1-26044436-G-C		Inborn genetic diseases	Uncertain significance (Jun 10, 2024)
1-26045009-C-T		Zinc deficiency, transient neonatal	Pathogenic (Aug 24, 2012)
1-26045053-C-T		Zinc deficiency, transient neonatal	Uncertain significance (Jun 20, 2018)
1-26045107-T-C		Zinc deficiency, transient neonatal	Pathogenic (Dec 22, 2006)
1-26045122-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
1-26045141-T-C		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
1-26045188-C-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2024)
1-26045192-C-T		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A2	protein_coding	protein_coding	ENST00000374276	8	8882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0809	0.917	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.928	185	224	0.826	0.0000125	2421
Missense in Polyphen		58	89.66	0.64689		1031
Synonymous	0.231	94	96.9	0.970	0.00000604	762
Loss of Function	2.71	5	17.1	0.292	8.68e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Zinc deficiency, transient neonatal (TNZD) [MIM:608118]: A disorder occurring in breast-fed infants as a consequence of low milk zinc concentration in their nursing mothers, which cannot be corrected by maternal zinc supplementation. A large amount of zinc, an essential trace mineral, is required for normal growth particularly in infants, and breast milk normally contains adequate zinc to meet the requirement for infants up to 4 to 6 months of age. Zinc deficiency can lead to dermatitis, alopecia, decreased growth, and impaired immune function. The disorder shows autosomal dominant inheritance with incomplete penetrance. {ECO:0000269|PubMed:17065149, ECO:0000269|PubMed:22733820}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Zinc homeostasis;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc efflux and compartmentalization by the SLC30 family;Zinc transporters (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.409
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.105
• hipred: Y
• hipred_score: 0.570
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a2
• Phenotype: hematopoietic system phenotype; immune system 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: response to zinc ion;regulation of sequestering of zinc ion;positive regulation of sequestering of zinc ion;zinc ion transmembrane transport
• Cellular component: cytoplasm;lysosomal membrane;late endosome;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: zinc ion transmembrane transporter activity;protein binding