SLC39A7

solute carrier family 39 member 7, the group of Solute carrier family 39

Basic information

Region (hg38): 6:33200304-33204439

Previous symbols: [ "HKE4" ]

Links

ENSG00000112473 ∙ NCBI:7922 ∙ OMIM:601416 ∙ HGNC:4927 ∙ Uniprot:Q92504 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• agammaglobulinemia 9, autosomal recessive (Strong), mode of inheritance: AR
• agammaglobulinemia (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Agammaglobulinemia 9, autosomal recessive	AR	Allergy/Immunology/Infectious	The condition can involve immunologic dysfunction, including with recurrent bacterial infections, and early diagnosis can allow management (eg, with IVIG); HSCT has been described	Allergy/Immunology/Infectious; Dermatologic	30718914

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A7 gene.

• not provided (152 variants)
• Inborn genetic diseases (13 variants)
• Agammaglobulinemia 9, autosomal recessive (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A7 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	35	5	41
missense		1	69	2	4	76
nonsense		1	1			2
start loss						0
frameshift			5			5
inframe indel			6			6
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding				19	1	20
Total	0	2	82	56	10

Highest pathogenic variant AF is 0.0000263

Variants in SLC39A7

This is a list of pathogenic ClinVar variants found in the SLC39A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33200322-G-C		not specified	Uncertain significance (Nov 22, 2023)
6-33200424-T-C		not specified	Uncertain significance (Jan 24, 2024)
6-33200451-A-G		not specified	Uncertain significance (Aug 01, 2022)
6-33200758-T-G		RXRB-related disorder	Likely benign (May 13, 2019)
6-33201250-C-T			Uncertain significance (Oct 19, 2020)
6-33201264-G-GC			Uncertain significance (Jun 23, 2022)
6-33201272-C-A			Uncertain significance (Oct 12, 2022)
6-33201278-G-C			Likely benign (Nov 10, 2023)
6-33201288-C-A			Uncertain significance (Nov 08, 2022)
6-33201295-C-A			Uncertain significance (Apr 13, 2022)
6-33201298-G-A			Likely pathogenic (Jun 01, 2019)
6-33201315-C-T			Likely benign (Nov 02, 2022)
6-33201318-G-A			Uncertain significance (Dec 07, 2023)
6-33201329-C-T			Likely benign (Feb 08, 2021)
6-33201329-C-CG			Uncertain significance (Mar 03, 2022)
6-33201334-G-C		not specified	Conflicting classifications of pathogenicity (Mar 13, 2023)
6-33201344-C-T			Likely benign (Oct 05, 2023)
6-33201347-G-T			Likely benign (Nov 07, 2023)
6-33201393-T-C		not specified	Uncertain significance (Sep 29, 2023)
6-33201397-A-G			Uncertain significance (May 06, 2022)
6-33201397-A-T			Uncertain significance (Aug 09, 2022)
6-33201405-T-C			Benign/Likely benign (Feb 01, 2024)
6-33201409-ACCATGGCCACAGCCATGC-A			Uncertain significance (Mar 24, 2021)
6-33201409-ACCATGGCCACAGCCATGCCCATGG-A			Uncertain significance (Aug 22, 2022)
6-33201409-A-ACCATGGCCACAGCCATGCCCATGG			Uncertain significance (Jul 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A7	protein_coding	protein_coding	ENST00000374677	7	3995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0821	0.916	124765	0	33	124798	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	198	269	0.737	0.0000141	3020
Missense in Polyphen		52	84.666	0.61418		980
Synonymous	2.38	77	109	0.709	0.00000579	1011
Loss of Function	2.72	5	17.1	0.292	7.96e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000171	0.000158
Ashkenazi Jewish	0.000504	0.000497
East Asian	0.0000557	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000165	0.000159
Middle Eastern	0.0000557	0.0000556
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Zinc transporter, that transports Zn(2+) from the endoplasmic reticulum/Golgi apparatus to the cytosol. Transport is stimulated by growth factors, such as EGF, and Ca(2+), as well as by exogenous Zn(2+). {ECO:0000269|PubMed:14525538, ECO:0000269|PubMed:15705588, ECO:0000269|PubMed:22317921}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Zinc influx into cells by the SLC39 gene family;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 transporters (Consensus)

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.374
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a7
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton 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); limbs/digits/tail phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: slc39a7
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: cellular zinc ion homeostasis;zinc ion transmembrane transport
• Cellular component: nucleoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;membrane;integral component of membrane
• Molecular function: zinc ion transmembrane transporter activity;protein binding