GRCh38/hg38 15q13.1-13.3(chr15:28918473-32149250)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
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:: RCV000052412.5

Allele description [Variation Report for GRCh38/hg38 15q13.1-13.3(chr15:28918473-32149250)x1]

GRCh38/hg38 15q13.1-13.3(chr15:28918473-32149250)x1

Genes:

LOC106736480:15q13 proximal microdeletion recombination region [Gene]
LOC106736465:15q13.2 beta inversion distal recombination region [Gene]
LOC106736464:15q13.2 beta inversion proximal recombination region [Gene]
LOC106736468:15q13.2-13.3 gamma inversion proximal recombination region [Gene]
ARHGAP11B-DT:ARHGAP11B divergent transcript [Gene - HGNC]
LOC130056725:ATAC-STARR-seq lymphoblastoid active region 9166 [Gene]
LOC130056726:ATAC-STARR-seq lymphoblastoid silent region 6267 [Gene]
LOC130056727:ATAC-STARR-seq lymphoblastoid silent region 6268 [Gene]
LOC126862088:BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 [Gene]
LOC126862086:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:30052673-30053872 [Gene]
LOC126862087:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:30226175-30227374 [Gene]
CHRFAM7A:CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion [Gene - OMIM - HGNC]
FAN1:FANCD2 and FANCI associated nuclease 1 [Gene - OMIM - HGNC]
KLF13:KLF transcription factor 13 [Gene - OMIM - HGNC]
LOC127829159:KLF13 promoter region [Gene]
LOC128899998:KLF13-II enhancer [Gene]
LOC128899999:KLF13-III enhancer [Gene]
LOC126862089:MED14-independent group 3 enhancer GRCh37_chr15:31442413-31443612 [Gene]
LOC129390677:MPRA-validated peak2281 silencer [Gene]
LOC129390678:MPRA-validated peak2283 silencer [Gene]
LOC129390679:MPRA-validated peak2284 silencer [Gene]
LOC129390680:MPRA-validated peak2285 silencer [Gene]
LOC129390681:MPRA-validated peak2289 silencer [Gene]
NSMCE3:NSE3 homolog, SMC5-SMC6 complex component [Gene - OMIM - HGNC]
OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
LOC126862085:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:30010173-30011372 [Gene]
ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
LOC125078053:Sharpr-MPRA regulatory region 11410 [Gene]
LOC125078052:Sharpr-MPRA regulatory region 13292 [Gene]
LOC112272581:Sharpr-MPRA regulatory region 3573 [Gene]
LOC112272582:Sharpr-MPRA regulatory region 5138 [Gene]
LOC121847941:Sharpr-MPRA regulatory region 8183 [Gene]
LOC125078051:Sharpr-MPRA regulatory region 8593 [Gene]
LOC110121498:VISTA enhancer hs2231 [Gene]
APBA2:amyloid beta precursor protein binding family A member 2 [Gene - OMIM - HGNC]
CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
LOC106736477:distal CHRNA7 low-copy repeat recombination region [Gene]
ENTREP2:endosomal transmembrane epsin interactor 2 [Gene - OMIM - HGNC]
GOLGA8H:golgin A8 family member H [Gene - HGNC]
GOLGA8J:golgin A8 family member J [Gene - HGNC]
GOLGA8Q:golgin A8 family member Q [Gene - HGNC]
GOLGA8R:golgin A8 family member R [Gene - HGNC]
GOLGA8T:golgin A8 family member T [Gene - HGNC]
LINC02249:long intergenic non-protein coding RNA 2249 [Gene - HGNC]
LINC02352:long intergenic non-protein coding RNA 2352 [Gene - HGNC]
LINC03034:long intergenic non-protein coding RNA 3034 [Gene - HGNC]
LCIIAR:lung cancer immune cell infiltration associated lncRNA [Gene - HGNC]
MIR211:microRNA 211 [Gene - OMIM - HGNC]
MTMR10:myotubularin related protein 10 [Gene - HGNC]
LOC106783506:nonconserved acetylation island sequence 49 enhancer [Gene]
LOC106736476:proximal CHRNA7 low-copy repeat recombination region [Gene]
TJP1:tight junction protein 1 [Gene - OMIM - HGNC]
TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

15q13.1-13.3

Genomic location:

Preferred name:

GRCh38/hg38 15q13.1-13.3(chr15:28918473-32149250)x1

HGVS:

NC_000015.10:g.(?_28918473)_(32149250_?)del
NC_000015.8:g.(?_26997968)_(30228743_?)del
NC_000015.9:g.(?_29210676)_(32441451_?)del

Links:

dbVar: nssv579721; dbVar: nsv531121

Observations:

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Paraleius sp. 4 SS-2020 voucher Pop55B_04 small subunit ribosomal RNA gene, part...
Paraleius sp. 4 SS-2020 voucher Pop55B_04 small subunit ribosomal RNA gene, partial sequence
gi|1835707610|gb|MT406351.1|

Nucleotide
Paraleius sp. 4 SS-2020 isolate Pop55B_01 cytochrome c oxidase subunit I (COX1) ...
Paraleius sp. 4 SS-2020 isolate Pop55B_01 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial
gi|1841307393|gb|MT462270.1|

Nucleotide
protein phosphatase 2, regulatory subunit B, gamma isoform X1 [Homo sapiens]
protein phosphatase 2, regulatory subunit B, gamma isoform X1 [Homo sapiens]
gi|2462597954|ref|XP_054206359.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000079764	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	de novo	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

SCV000079764

GeneDx

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

de novo

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	de novo	yes	1	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

Details of each submission

From GeneDx, SCV000079764.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	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	de novo	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

ClinVar

Relating variation to medicine