VCV000183383.1 - ClinVar

NC_000002.10:g.148447496_149377297del

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

NC_000002.10:g.148447496_149377297del

Variation ID: 183383 Accession: VCV000183383.1

Type and length

Deletion, 929,802 bp

Location

Cytogenetic: 2q23.1 2: 147973457-148903258 (GRCh38) [ NCBI UCSC ] 2: 148731026-149660827 (GRCh37) [ NCBI UCSC ] 2: 148447496-149377297 (NCBI36) [ 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	Mar 16, 2015	Mar 16, 2015	Jun 1, 2014

HGVS

Nucleotide	Protein	Molecular consequence
NC_000002.12:g.147973457_148903258del
NC_000002.11:g.148731026_149660827del
NC_000002.10:g.148447496_149377297del

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

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.
MBD5		Sufficient evidence for dosage pathogenicity	Little evidence for dosage pathogenicity	GRCh38 GRCh37	1556	1635
EPC2		-	-	GRCh38 GRCh37	42	73
KIF5C		-	-	GRCh38 GRCh38	239	259
LOC126806366	-	-	-	GRCh38	-	17
LOC126806367	-	-	-	GRCh38	-	13
LOC129934887	-	-	-	GRCh38	-	16
LOC129934888	-	-	-	GRCh38	-	17
LOC129934889	-	-	-	GRCh38	-	9
LOC129934890	-	-	-	GRCh38	-	9
LOC129934891	-	-	-	GRCh38	-	9

There are 7 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37 , NCBI36) and ClinGen Dosage Sensitivity Map.

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.
Intellectual disability, autosomal dominant 1	Pathogenic (1)	no assertion criteria provided	Jun 1, 2014	RCV000162197.3

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 (Jun 01, 2014)	no assertion criteria provided Method: research	2q23.1 deletion syndrome Affected status: yes Allele origin: de novo	Elsea Lab, Dept of Molecular and Human Genetics, Baylor College of Medicine Accession: SCV000172261.1 First in ClinVar: Mar 16, 2015 Last updated: Mar 16, 2015	Publications: PubMed (2) PubMed: 21981781‚ 19904302 Number of individuals with the variant: 1 Age: 6-12 years Sex: female Ethnicity/Population group: Caucasian

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
MBD5 haploinsufficiency is associated with sleep disturbance and disrupts circadian pathways common to Smith-Magenis and fragile X syndromes.	Mullegama SV	European journal of human genetics : EJHG	2015	PMID: 25271084
Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder.	Talkowski ME	American journal of human genetics	2011	PMID: 21981781
Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures.	Williams SR	European journal of human genetics : EJHG	2010	PMID: 19904302

Text-mined citations for this variant ...

Record last updated Oct 15, 2023

ClinVar Genomic variation as it relates to human health

NC_000002.10:g.148447496_149377297del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...