VCV000001104.2 - ClinVar

NM_000642.3(AGL):c.1999del (p.Gln667fs)

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_000642.3(AGL):c.1999del (p.Gln667fs)

Variation ID: 1104 Accession: VCV000001104.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 1p21.2 1: 99881175 (GRCh38) [ NCBI UCSC ] 1: 100346731 (GRCh37) [ NCBI UCSC ]

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	Jul 25, 2015	Jul 25, 2015	Jul 31, 2000

HGVS

Nucleotide	Protein	Molecular consequence
NM_000642.3:c.1999del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000633.2:p.Gln667fs	frameshift
NM_000028.3:c.1999delC	NP_000019.2:p.Gln667Argfs	frameshift
NM_000643.3:c.1999delC	NP_000634.2:p.Gln667Argfs	frameshift
NM_000644.3:c.1999delC	NP_000635.2:p.Gln667Argfs	frameshift
NM_000646.3:c.1951delC	NP_000637.2:p.Gln651Argfs	frameshift
NM_001425325.1:c.1999delC	NP_001412254.1:p.Gln667Argfs	frameshift
NM_001425326.1:c.1999delC	NP_001412255.1:p.Gln667Argfs	frameshift
NM_001425327.1:c.1798delC	NP_001412256.1:p.Gln600Argfs	frameshift
NM_001425328.1:c.1795delC	NP_001412257.1:p.Gln599Argfs	frameshift
NM_001425329.1:c.1795delC	NP_001412258.1:p.Gln599Argfs	frameshift
NM_001425332.1:c.1621delC	NP_001412261.1:p.Gln541Argfs	frameshift
NC_000001.11:g.99881175del
NC_000001.10:g.100346731del
NG_012865.1:g.36092del

... more HGVS ... less HGVS

Protein change

Q651fs, Q667fs

Other names

Canonical SPDI

NC_000001.11:99881174:C:

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

ClinGen: CA114764 OMIM: 610860.0011 dbSNP: rs387906246 VarSome

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.
AGL		-	-	GRCh38 GRCh37	2675	2695

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.
Glycogen storage disease IIIb	Pathogenic (1)	no assertion criteria provided	Jul 31, 2000	RCV000001163.12

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 (Jul 31, 2000)	no assertion criteria provided Method: literature only	GLYCOGEN STORAGE DISEASE, TYPE IIIb Affected status: not provided Allele origin: germline	OMIM Accession: SCV000021313.3 First in ClinVar: Apr 04, 2013 Last updated: Jul 25, 2015	Publications: PubMed (1) PubMed: 10925384 Comment on evidence: In a 2-year-old patient of mixed Asian ancestry with glycogen storage disease type IIIb (GSD3B; 232400), Okubo et al. (2000) observed compound heterozygosity for 2 … (more) In a 2-year-old patient of mixed Asian ancestry with glycogen storage disease type IIIb (GSD3B; 232400), Okubo et al. (2000) observed compound heterozygosity for 2 mutations in the AGL gene: a deletion of 2399C in exon 16 inherited from the Japanese father, and a G-to-A transition at position +5 at the donor splice site of intron 33 (610860.0012) inherited from the Chinese mother. The girl had been admitted to hospital because of liver dysfunction. Hepatomegaly was first noted at age 4 months. She had experienced occasional hypoglycemia, and growth retardation was noted. Muscular manifestations were not described. (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
Compound heterozygous patient with glycogen storage disease type III: identification of two novel AGL mutations, a donor splice site mutation of Chinese origin and a 1-bp deletion of Japanese origin.	Okubo M	American journal of medical genetics	2000	PMID: 10925384

Text-mined citations for rs387906246 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_000642.3(AGL):c.1999del (p.Gln667fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs387906246 ...