SLC30A1

solute carrier family 30 member 1, the group of Solute carrier family 30

Basic information

Region (hg38): 1:211571568-211579161

Previous symbols: [ "ZNT1" ]

Links

ENSG00000170385 ∙ NCBI:7779 ∙ OMIM:609521 ∙ HGNC:11012 ∙ Uniprot:Q9Y6M5 ∙ 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 SLC30A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A1 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SLC30A1

This is a list of pathogenic ClinVar variants found in the SLC30A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-211575409-T-G		not specified	Uncertain significance (Nov 25, 2024)
1-211575438-C-G		not specified	Uncertain significance (Feb 27, 2023)
1-211575488-T-C		not specified	Uncertain significance (Feb 13, 2024)
1-211575548-G-C		not specified	Uncertain significance (May 23, 2023)
1-211575855-T-C		not specified	Uncertain significance (Oct 29, 2024)
1-211576008-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-211576080-C-G		not specified	Uncertain significance (Aug 07, 2024)
1-211576088-C-A		not specified	Uncertain significance (Mar 06, 2023)
1-211576242-C-T		not specified	Uncertain significance (Dec 25, 2024)
1-211576281-T-A		not specified	Uncertain significance (Apr 01, 2024)
1-211576287-G-T		not specified	Uncertain significance (Nov 11, 2024)
1-211578013-G-C		not specified	Uncertain significance (Sep 22, 2023)
1-211578021-T-G		not specified	Uncertain significance (Nov 07, 2023)
1-211578086-T-C		not specified	Uncertain significance (Jan 21, 2025)
1-211578240-G-C		not specified	Uncertain significance (Apr 07, 2023)
1-211578471-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-211578515-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-211578591-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-211578592-G-C		not specified	Uncertain significance (Apr 04, 2024)
1-211578605-C-T		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A1	protein_coding	protein_coding	ENST00000367001	2	7175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0147	122679	0	1	122680	0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	183	288	0.635	0.0000132	3306
Missense in Polyphen		31	106.05	0.29231		1204
Synonymous	0.653	105	114	0.922	0.00000553	1056
Loss of Function	3.32	0	12.8	0.00	6.09e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in zinc transport out of the cell.
• Pathway: Mineral absorption - Homo sapiens (human);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: 0.210

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.458
• hipred: Y
• hipred_score: 0.664
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a1
• Phenotype: reproductive system 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); embryo phenotype

Gene ontology

• Biological process: in utero embryonic development;zinc ion transport;cellular calcium ion homeostasis;cellular zinc ion homeostasis;negative regulation of neurotransmitter secretion;calcium ion import;cadmium ion transmembrane transport;zinc ion transmembrane transport;negative regulation of zinc ion transmembrane import;detoxification of cadmium ion;negative regulation of calcium ion import
• Cellular component: cytoplasm;endoplasmic reticulum;Golgi apparatus;plasma membrane;T-tubule;nuclear membrane;Schaffer collateral - CA1 synapse;integral component of postsynaptic density membrane
• Molecular function: zinc ion transmembrane transporter activity;protein binding;calcium channel inhibitor activity