VCV000010947.1 - ClinVar

NM_001128127.3(GK):c.338-52_338-51insAluY

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001128127.3(GK):c.338-52_338-51insAluY

Variation ID: 10947 Accession: VCV000010947.1

Type and length

Insertion, -

Location

Cytogenetic: Xp21.3-p21.2 -

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 25, 2014	Feb 25, 2014	Jan 1, 2000

HGVS

Nucleotide	Protein	Molecular consequence
NG_008178.1:g.42713_42714insAluY
LRG_848:g.42713_42714insAluY

Protein change

Other names

ALU INS, IVS4

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

OMIM: 300474.0007

Comment on variant

Insertion of 316-nt AluY sequence into intron 4 of gene GK.

NCBI staff provided an HGVS expression for allelic variant 300474.0007 based on the published description: IVS4-52ins316alu (Zhang et al., 2000; PubMed 10737976). The insert is more complex than that, including a duplication of the sequence CTTATTTTTT at both ends (Figure 2B).

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.
GK		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	72	249

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.
Inborn glycerol kinase deficiency	Pathogenic (1)	no assertion criteria provided	Jan 1, 2000	RCV000011694.3

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 (Jan 01, 2000)	no assertion criteria provided Method: literature only	GLYCEROL KINASE DEFICIENCY Affected status: not provided Allele origin: germline	OMIM Accession: SCV000031926.2 First in ClinVar: Apr 04, 2013 Last updated: Feb 25, 2014	Publications: PubMed (1) PubMed: 10737976 Comment on evidence: Zhang et al. (2000) reported the case of a male with benign glycerol kinase deficiency (GKD; 307030) who was incidentally identified after observation of pseudohypertriglyceridemia … (more) Zhang et al. (2000) reported the case of a male with benign glycerol kinase deficiency (GKD; 307030) who was incidentally identified after observation of pseudohypertriglyceridemia at the age of 36 years. DNA sequencing of the GK gene showed insertion of an AluY sequence in intron 4 (IVS4-52ins316Alu) of the glycerol kinase gene. Although Alu insertions had been implicated in other disorders, and a closely related AluY element had been found as an insert in the C1 inhibitor gene (606860) in patients with hereditary angioedema (106100), this was the first case of glycerol kinase deficiency caused by an Alu insertion. (less)

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
AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency.	Zhang Y	Human mutation	2000	PMID: 10737976

Text-mined citations for this variant ...

Record last updated Jun 17, 2023

ClinVar Genomic variation as it relates to human health

NM_001128127.3(GK):c.338-52_338-51insAluY

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...