VCV000007631.1 - ClinVar

NC_000004.12:g.(68323330_?)_(?_68725531)del

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.

association

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000004.12:g.(68323330_?)_(?_68725531)del

Variation ID: 7631 Accession: VCV000007631.1

Type and length

Deletion, -

Location

Cytogenetic: 4q13 -

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	Apr 4, 2013	Apr 4, 2013	Dec 1, 2008

HGVS

Nucleotide	Protein	Molecular consequence
NC_000004.12:g.(68323330_?)_(?_68725531)del
NC_000004.10:g.(68871643_?)_(?_69625838)del

Protein change

Other names

150-KB DEL

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

dbVar: nssv1415006 dbVar: nsv513778 OMIM: 601903.0001

Comment on variant

NCBI staff provided HGVS expressions for allelic variant 601903.0001 after determining that the locations reported in the paper by Yang et al., 2008 (PubMed 18992858) corresponded to NCBI36.

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.
UGT2B17		-	-	GRCh38 GRCh37	57	86

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.
Bone mineral density quantitative trait locus 12	association (1)	no assertion criteria provided	Dec 1, 2008	RCV000008070.2

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.
association (Dec 01, 2008)	no assertion criteria provided Method: literature only	BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 12 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000028275.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 18992858 Comment on evidence: In a case-control genomewide analysis of copy number variation (CNV) in 350 elderly Chinese individuals with osteoporosis-related hip fracture (BMND12; 612560) and 350 geography- and … (more) In a case-control genomewide analysis of copy number variation (CNV) in 350 elderly Chinese individuals with osteoporosis-related hip fracture (BMND12; 612560) and 350 geography- and age-matched controls, Yang et al. (2008) found CNV on chromosome 4q13.2 to be strongly associated with osteoporotic fracture (p = 2.0 x 10(-4), corrected p = 0.02; odds ratio = 1.73). Using PCR and electrophoresis as well as real-time PCR in 60 Chinese individuals, 20 for each copy-number genotype predicted by the Affymetrix copy number analysis tool (CNAT), the authors identified a 150-kb deleted interval at chromosome 4q13.2 spanning the entire UGT2B17 gene. The authors replicated the association between UGT2B17 CNV and osteoporotic fracture in an independent Chinese sample of 399 cases with osteoporosis-related hip fracture and 400 age-matched controls (p = 6.34 x 10(-3)), and demonstrated an increased risk of osteoporotic fracture in individuals with an existing UGT2B17 gene (odds ratio = 1.58; p = 0.01). Yang et al. (2008) also found consistently significant association between UGT2B17 CNV and major risk factors for osteoporotic fracture in an independent sample of 689 Chinese and 1,000 Caucasian individuals, and in an independent sample of 236 young Chinese males, they demonstrated that individuals without UGT2B17 had significantly higher concentrations of testosterone and estradiol. (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
Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis.	Yang TL	American journal of human genetics	2008	PMID: 18992858

Text-mined citations for this variant ...

Record last updated Dec 02, 2023

ClinVar Genomic variation as it relates to human health

NC_000004.12:g.(68323330_?)_(?_68725531)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...