VCV000006648.1 - ClinVar

NM_005677.4:c.107_321del

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_005677.4:c.107_321del

Variation ID: 6648 Accession: VCV000006648.1

Type and length

Deletion, -

Location

Cytogenetic: 3p25 -

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	May 1, 2015	May 1, 2015	Aug 4, 1998

HGVS

Nucleotide	Protein	Molecular consequence
NM_005677.4:c.107_321del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.

Protein change

Other names

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: 603033.0001

Comment on variant

The genomic location for allelic variant 603033.0001 will not be computed from alignment of the transcript sequence to the genome until there is experimental evidence for the genomic basis of the loss of exons 2 and 3 from the transcript.

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.
COLQ		-	-	GRCh38 GRCh37	578	604

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.
Congenital myasthenic syndrome 5	Pathogenic (1)	no assertion criteria provided	Aug 4, 1998	RCV000007027.3

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 (Aug 04, 1998)	no assertion criteria provided Method: literature only	MYASTHENIC SYNDROME, CONGENITAL, 5 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000027223.2 First in ClinVar: Apr 04, 2013 Last updated: May 01, 2015	Publications: PubMed (1) PubMed: 9689136 Comment on evidence: In a patient with congenital myasthenic syndrome-5 (CMS5; 603034), Ohno et al. (1998) found compound heterozygous mutations in the COLQ gene: a deletion of 215 … (more) In a patient with congenital myasthenic syndrome-5 (CMS5; 603034), Ohno et al. (1998) found compound heterozygous mutations in the COLQ gene: a deletion of 215 basepairs following nucleotide 107 of the COLQ gene and an E214X substitution (603033.0002). The deletion was caused by skipping of exons 2 and 3, causing a frameshift after codon 35. The mutation abolished the proline-rich attachment domain (PRAD) and predicted 25 missense codons followed by a stop codon. The deletion mutation was inherited from the mother and the truncating mutation from the father. (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
Human endplate acetylcholinesterase deficiency caused by mutations in the collagen-like tail subunit (ColQ) of the asymmetric enzyme.	Ohno K	Proceedings of the National Academy of Sciences of the United States of America	1998	PMID: 9689136

Text-mined citations for this variant ...

Record last updated Oct 01, 2022

ClinVar Genomic variation as it relates to human health

NM_005677.4:c.107_321del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...