SLC39A7
Basic information
Region (hg38): 6:33200305-33204439
Previous symbols: [ "HKE4" ]
Links
Phenotypes
GenCC
Source:
- agammaglobulinemia 9, autosomal recessive (Strong), mode of inheritance: AR
- agammaglobulinemia (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
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
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 | 48 | 54 | ||||
missense | 76 | 84 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 6 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 4 | 5 | |||
non coding | 22 | 23 | ||||
Total | 0 | 4 | 91 | 73 | 9 |
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 (Aug 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:
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:
- 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