SLC30A5

solute carrier family 30 member 5, the group of Solute carrier family 30

Basic information

Region (hg38): 5:69093990-69131069

Links

ENSG00000145740 ∙ NCBI:64924 ∙ OMIM:607819 ∙ HGNC:19089 ∙ Uniprot:Q8TAD4 ∙ 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 SLC30A5 gene.

• Inborn genetic diseases (18 variants)
• not provided (6 variants)
• Hydrops fetalis;Noncompaction cardiomyopathy;Severe hydrops fetalis;Concentric hypertrophic cardiomyopathy;Hypertrophic cardiomyopathy (1 variants)
• Hypertrophic cardiomyopathy;Noncompaction cardiomyopathy;Hydrops fetalis;Severe hydrops fetalis;Concentric hypertrophic cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A5 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
missense			17	1	1	19
nonsense			1			1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	2	18	1	3

Variants in SLC30A5

This is a list of pathogenic ClinVar variants found in the SLC30A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-69094286-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-69100936-G-A			Benign (May 30, 2017)
5-69100937-T-TG			Benign (Aug 16, 2018)
5-69103062-G-T			Benign (May 30, 2017)
5-69104669-T-G		not specified	Uncertain significance (Jun 24, 2022)
5-69108399-G-C		not specified	Uncertain significance (Nov 09, 2022)
5-69113204-T-A		not specified	Uncertain significance (Oct 27, 2022)
5-69114461-A-G		not specified	Uncertain significance (Dec 28, 2022)
5-69115243-G-A		not specified	Uncertain significance (Dec 13, 2023)
5-69115309-G-C		not specified	Uncertain significance (Jun 06, 2023)
5-69115312-G-A		not specified	Uncertain significance (Nov 28, 2023)
5-69115315-G-A		not specified	Uncertain significance (Oct 20, 2021)
5-69115316-T-C		not specified	Uncertain significance (Oct 03, 2022)
5-69115343-T-G			Uncertain significance (Nov 13, 2023)
5-69115349-A-T		not specified	Uncertain significance (Feb 09, 2023)
5-69115369-T-G		not specified	Uncertain significance (Jun 21, 2022)
5-69115971-GTTATC-G		Hypertrophic cardiomyopathy;Hydrops fetalis;Noncompaction cardiomyopathy;Severe hydrops fetalis;Concentric hypertrophic cardiomyopathy	Likely pathogenic (Jan 29, 2020)
5-69116004-G-A		not specified	Uncertain significance (Jan 02, 2024)
5-69116029-T-C		not specified	Uncertain significance (Dec 21, 2023)
5-69116041-A-G		not specified	Uncertain significance (May 04, 2022)
5-69116056-G-T		not specified	Uncertain significance (Aug 17, 2021)
5-69116424-G-C		not specified	Uncertain significance (May 31, 2023)
5-69116448-G-A		not specified	Uncertain significance (Feb 12, 2024)
5-69116471-C-G		not specified	Uncertain significance (Jan 04, 2024)
5-69116562-G-A		not specified	Likely benign (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A5	protein_coding	protein_coding	ENST00000396591	16	37424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0681	0.932	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	281	393	0.714	0.0000189	5016
Missense in Polyphen		42	90.909	0.462		1153
Synonymous	0.972	124	139	0.895	0.00000720	1499
Loss of Function	4.00	9	34.2	0.263	0.00000172	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.000352	0.000298
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000423	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a zinc transporter. May be a transporter of zinc into beta cells in order to form insulin crystals. Partly regulates cellular zinc homeostasis. Required with ZNT7 for the activation of zinc-requiring enzymes, alkaline phosphatases (ALPs). Transports zinc into the lumens of the Golgi apparatus and vesicular compartments where ALPs locate, thus, converting apoALPs to holoALPs. Required with ZNT6 and ZNT7 for the activation of TNAP. {ECO:0000269|PubMed:11904301, ECO:0000269|PubMed:11937503, ECO:0000269|PubMed:15276077, ECO:0000269|PubMed:15525635, ECO:0000269|PubMed:15994300}.
• 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: 0.132

Intolerance Scores

• loftool: 0.592
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.619
• hipred: Y
• hipred_score: 0.639
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.320

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc30a5
• Phenotype: skeleton phenotype; limbs/digits/tail 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: cobalt ion transport;zinc ion transport;cellular zinc ion homeostasis;response to zinc ion;regulation of proton transport;zinc ion transmembrane transport
• Cellular component: nucleus;nucleolus;Golgi apparatus;integral component of plasma membrane;membrane;apical plasma membrane;secretory granule;secretory granule membrane
• Molecular function: zinc ion transmembrane transporter activity;zinc ion binding