VCV000424757.4 - ClinVar

NM_022154.5(SLC39A8):c.[97G>A;1004G>C];[c.610G>T]

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

This genotype includes the following haplotypes

NM_022154.5(SLC39A8):c.[97G>A;1004G>C];[c.610G>T]

Other names: -
Functional consequence: -
Links: -

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LOC126807125	-	-	-	GRCh38	-	57
LOC129992876	-	-	-	GRCh38	-	25
SLC39A8		-	-	GRCh38 GRCh37	116	214

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
SLC39A8-CDG	Pathogenic (1)	criteria provided, single submitter	Nov 3, 2015	RCV001848855.11

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Nov 03, 2015)	criteria provided, single submitter (Park et al. (AJHG 2015)) Method: research	SLC39A8 deficiency Affected status: yes Allele origin: germline	Metabolic Research Unit, Children's University Hospital Muenster Accession: SCV000256231.3 First in ClinVar: Jan 09, 2016 Last updated: Jan 09, 2016 Comment: The mother was heterozygous for the c.610G>T variant, and the father was heterozygous for the c.97G>A and c.1004G>C variants.	Publications: PubMed (1) PubMed: 26637979 Number of individuals with the variant: 1 Sex: female Geographic origin: Europe

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
The Impact of ZIP8 Disease-Associated Variants G38R, C113S, G204C, and S335T on Selenium and Cadmium Accumulations: The First Characterization.	Liang ZL	International journal of molecular sciences	2021	PMID: 34768831
The schizophrenia risk locus in SLC39A8 alters brain metal transport and plasma glycosylation.	Mealer RG	Scientific reports	2020	PMID: 32753748
Functional analysis of SLC39A8 mutations and their implications for manganese deficiency and mitochondrial disorders.	Choi EK	Scientific reports	2018	PMID: 29453449
SLC39A8 deficiency: biochemical correction and major clinical improvement by manganese therapy.	Park JH	Genetics in medicine : official journal of the American College of Medical Genetics	2018	PMID: 28749473
SLC39A8 Deficiency: A Disorder of Manganese Transport and Glycosylation.	Park JH	American journal of human genetics	2015	PMID: 26637979
SLC39A8 Deficiency: A Disorder of Manganese Transport and Glycosylation.	Park JH	American journal of human genetics	2015	PMID: 26637979
SLC39A8 Deficiency: A Disorder of Manganese Transport and Glycosylation.	Park JH	American journal of human genetics	2015	PMID: 26637979
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC39A8	-	-	-	-

Text-mined citations for this variant ...

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_022154.5(SLC39A8):c.[97G>A;1004G>C];[c.610G>T]

Variant Details

NM_022154.5(SLC39A8):c.[97G>A;1004G>C];[c.610G>T]

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...