SLC30A7

solute carrier family 30 member 7, the group of Solute carrier family 30

Basic information

Region (hg38): 1:100896076-100996260

Links

ENSG00000162695

∙ NCBI:148867 ∙ OMIM:611149 ∙ HGNC:19306 ∙ Uniprot:Q8NEW0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Joubert syndrome (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ziegler-Huang syndrome	AR	Allergy/Immunology/Infectious; Endocrine; Hematologic	The condition can include hormone deficiencies, and awareness may allow medical management; Due to mineral abnormalities, supplementation has been described as necessary; The condition may involve bone marrow failure, including neutropenia and thrombocytopenia, and the need for interventions such as RBC transfusions has been described	Allergy/Immunology/Infectious; Endocrine; Hematologic	36821639

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC30A7 gene.

not_specified (48 variants)
not_provided (19 variants)
Ziegler-Huang_syndrome (3 variants)
Decreased_testicular_size (1 variants)
Severe_early-onset_pulmonary_alveolar_proteinosis_due_to_MARS_deficiency (1 variants)
Testicular_atrophy (1 variants)
Joubert_syndrome_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000133496.5. 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				4 clinvar	1 clinvar	5
missense	1 clinvar		50 clinvar	2 clinvar	1 clinvar	54
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	1	2	50	6	2

Highest pathogenic variant AF is 0.000011628797

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC30A7	protein_coding	protein_coding	ENST00000370112	11	85678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.40e-7	0.841	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.467	182	201	0.907	0.00000921	2485
Missense in Polyphen		72	83.253	0.86483		1068
Synonymous	-0.435	79	74.2	1.06	0.00000393	718
Loss of Function	1.49	13	20.2	0.643	8.56e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000212	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to facilitate zinc transport from the cytoplasm into the Golgi apparatus. Partly regulates cellular zinc homeostasis. Required with ZNT5 for the activation of zinc- requiring enzymes, alkaline phosphatases (ALPs). Transports zinc into the lumens of the Golgi apparatus and the vesicular compartments where ALPs locate, thus, converting apoALPs to holoALPs. Required with ZNT5 and ZNT6 for the activation of TNAP (By similarity). {ECO:0000250, ECO:0000269|PubMed:15276077, 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: 0.122

Intolerance Scores

loftool: 0.740
rvis_EVS: -0.69
rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

pHI: 0.319
hipred: Y
hipred_score: 0.544
ghis: 0.649

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.786

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc30a7
Phenotype: 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); homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype;

Gene ontology

Biological process: zinc ion transport;sequestering of zinc ion;cation transmembrane transport
Cellular component: cytoplasm;Golgi apparatus;integral component of membrane;cytoplasmic vesicle;vesicle;perinuclear region of cytoplasm
Molecular function: cation transmembrane transporter activity