GRCh38/hg38 15q11.2(chr15:22572809-23174546)x1 AND See cases

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 12, 2011
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000050507.9

Allele description [Variation Report for GRCh38/hg38 15q11.2(chr15:22572809-23174546)x1]

GRCh38/hg38 15q11.2(chr15:22572809-23174546)x1

Genes:

LOC130056712:ATAC-STARR-seq lymphoblastoid active region 9154 [Gene]
LOC130056713:ATAC-STARR-seq lymphoblastoid active region 9155 [Gene]
LOC130056714:ATAC-STARR-seq lymphoblastoid active region 9156 [Gene]
LOC130056715:ATAC-STARR-seq lymphoblastoid active region 9157 [Gene]
LOC130056716:ATAC-STARR-seq lymphoblastoid active region 9158 [Gene]
LOC130056717:ATAC-STARR-seq lymphoblastoid active region 9159 [Gene]
LOC130056718:ATAC-STARR-seq lymphoblastoid active region 9160 [Gene]
LOC130056707:ATAC-STARR-seq lymphoblastoid silent region 6257 [Gene]
LOC130056708:ATAC-STARR-seq lymphoblastoid silent region 6258 [Gene]
LOC130056709:ATAC-STARR-seq lymphoblastoid silent region 6259 [Gene]
LOC130056710:ATAC-STARR-seq lymphoblastoid silent region 6260 [Gene]
LOC130056711:ATAC-STARR-seq lymphoblastoid silent region 6261 [Gene]
LOC126862074:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:22990202-22991401 [Gene]
NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
NIPA2:NIPA magnesium transporter 2 [Gene - OMIM - HGNC]
LOC112272576:Sharpr-MPRA regulatory region 3977 [Gene]
LOC112272575:Sharpr-MPRA regulatory region 8478 [Gene]
CYFIP1:cytoplasmic FMR1 interacting protein 1 [Gene - OMIM - HGNC]
GOLGA6L1:golgin A6 family like 1 [Gene - HGNC]
TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
LOC283683:uncharacterized LOC283683 [Gene]

Variant type:

copy number loss

Cytogenetic location:

15q11.2

Genomic location:

Preferred name:

GRCh38/hg38 15q11.2(chr15:22572809-23174546)x1

Other names:

GRCh38/hg38 15q11.2(chr15:22572809-23066575)x1

HGVS:

NC_000015.10:g.(?_22572809)_(23066575_?)del
NC_000015.10:g.(?_22572809)_(23174546_?)del
NC_000015.10:g.(?_22572809)_(23066575_?)del
NC_000015.8:g.(?_20249886)_(20851728_?)del
NC_000015.9:g.(?_22698522)_(23300287_?)del

Links:

dbVar: nssv3395692; dbVar: nssv3396670; dbVar: nssv575460; dbVar: nssv575509; dbVar: nssv575776; dbVar: nssv576769; dbVar: nssv576799; dbVar: nssv576800; dbVar: nsv1067694; dbVar: nsv529157

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000077829	ISCA site 4 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Uncertain significance (Aug 12, 2011)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000175215	ISCA site 4 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Benign (May 27, 2010)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000077829

ISCA site 4

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Uncertain significance
(Aug 12, 2011)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000175215

ISCA site 4

See additional submitters

no assertion criteria provided

Benign
(May 27, 2010)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not provided	yes	11	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]

PMID:: 21844811
PMCID:: PMC3661946

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]

PMID:: 20466091
PMCID:: PMC2869000

Details of each submission

From ISCA site 4, SCV000077829.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)
2	not provided	1	not provided	not provided	clinical testing	PubMed (1)
3	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
2	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
3	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

From ISCA site 4, SCV000175215.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)
2	not provided	1	not provided	not provided	clinical testing	PubMed (1)
3	not provided	1	not provided	not provided	clinical testing	PubMed (1)
4	not provided	1	not provided	not provided	clinical testing	PubMed (1)
5	not provided	1	not provided	not provided	clinical testing	PubMed (1)
6	not provided	1	not provided	not provided	clinical testing	PubMed (1)
7	not provided	1	not provided	not provided	clinical testing	PubMed (1)
8	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
2	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
3	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
4	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
5	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
6	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
7	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
8	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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