VCV000157548.2 - ClinVar

NC_000007.14:g.156778086_156854056dup

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_000007.14:g.156778086_156854056dup

Variation ID: 157548 Accession: VCV000157548.2

Type and length

Duplication, 75,971 bp

Location

Cytogenetic: 7q36.3 7: 156778086-156854056 (GRCh38) [ NCBI UCSC ] 7: 156570780-156646750 (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	Oct 7, 2016	Apr 6, 2024	Oct 1, 2014

HGVS

Nucleotide	Protein	Molecular consequence
NC_000007.14:g.156778086_156854056dup
NC_000007.13:g.156570780_156646750dup

Protein change

Other names

75-KB DUP

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: nssv7487226 dbVar: nsv1197553 OMIM: 605522.0020 VarSome

Comment on variant

75-kb microduplication spanning exons 2-5 of LMBR1 plus flanking intronic sequences.

NCBI staff reviewed the sequence information reported in PubMed 24456159 Table 1 to determine the location of this allele on the current reference sequence.

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.
LMBR1		-	-	GRCh38 GRCh37	218	562
LOC129999724	-	-	-	GRCh38	-	47
LOC129999725	-	-	-	GRCh38	-	47
ZRS		-	-	GRCh38	-	122

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.
Laurin-Sandrow syndrome	Pathogenic (1)	no assertion criteria provided	Oct 1, 2014	RCV000144893.5

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 (Oct 01, 2014)	no assertion criteria provided Method: literature only	LAURIN-SANDROW SYNDROME Affected status: not provided Allele origin: germline	OMIM Accession: SCV000191895.3 First in ClinVar: Nov 09, 2014 Last updated: Apr 06, 2024	Publications: PubMed (1) PubMed: 24456159 Patil, S. J., Bhat, V. (more...) Patil, S. J., Bhat, V. Laurin-Sandrow syndrome: a case report. Newsl. Indian Acad. Med. Genet. 6: 3-5, 2013. Comment on evidence: In an Indian boy (family 3) with bilateral polysyndactyly of the hands, mirror-image polysyndactyly of the feet, absent tibia, and duplication of the fibula (LSS; … (more) In an Indian boy (family 3) with bilateral polysyndactyly of the hands, mirror-image polysyndactyly of the feet, absent tibia, and duplication of the fibula (LSS; 135750), Lohan et al. (2014) identified heterozygosity for an approximately 75-kb duplication involving the ZRS region in intron 5 as well as several exons of the LMBR1 gene (chr7:156,570,780-156,646,750, GRCh37). The patient, who was originally described by Patil and Bhat (2013), also exhibited mild facial dysmorphism, with underdeveloped alae nasi, broad nasal tip, and short grooved columella. (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
Microduplications encompassing the Sonic hedgehog limb enhancer ZRS are associated with Haas-type polysyndactyly and Laurin-Sandrow syndrome.	Lohan S	Clinical genetics	2014	PMID: 24456159
Patil, S. J., Bhat, V. Laurin-Sandrow syndrome: a case report. Newsl. Indian Acad. Med. Genet. 6: 3-5, 2013.	-	-	-	-

Text-mined citations for this variant ...

Record last updated Apr 06, 2024

ClinVar Genomic variation as it relates to human health

NC_000007.14:g.156778086_156854056dup

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...