GRCh38/hg38 15q13.2-13.3(chr15:30217122-32217725)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 4, 2013
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000141477.4

Allele description [Variation Report for GRCh38/hg38 15q13.2-13.3(chr15:30217122-32217725)x1]

GRCh38/hg38 15q13.2-13.3(chr15:30217122-32217725)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]
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]
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]
LOC129390679:MPRA-validated peak2284 silencer [Gene]
LOC129390680:MPRA-validated peak2285 silencer [Gene]
LOC129390681:MPRA-validated peak2289 silencer [Gene]
OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
LOC125078053:Sharpr-MPRA regulatory region 11410 [Gene]
LOC112272582:Sharpr-MPRA regulatory region 5138 [Gene]
LOC121847941:Sharpr-MPRA regulatory region 8183 [Gene]
LOC110121498:VISTA enhancer hs2231 [Gene]
CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
LOC106736477:distal CHRNA7 low-copy repeat recombination region [Gene]
GOLGA8H:golgin A8 family member H [Gene - HGNC]
GOLGA8Q:golgin A8 family member Q [Gene - HGNC]
GOLGA8R:golgin A8 family member R [Gene - HGNC]
LINC02352:long intergenic non-protein coding RNA 2352 [Gene - HGNC]
LINC03034:long intergenic non-protein coding RNA 3034 [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]
TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

15q13.2-13.3

Genomic location:

Preferred name:

GRCh38/hg38 15q13.2-13.3(chr15:30217122-32217725)x1

HGVS:

NC_000015.10:g.(?_30217122)_(32217725_?)del
NC_000015.8:g.(?_28296617)_(30297218_?)del
NC_000015.9:g.(?_30509325)_(32509926_?)del

Links:

dbVar: nssv3395564; dbVar: nsv994969

Observations:

Condition(s)

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

Recent activity

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AP-3 complex subunit beta-1 isoform X2 [Rattus norvegicus]
AP-3 complex subunit beta-1 isoform X2 [Rattus norvegicus]
gi|2678918023|ref|XP_063137774.1|

Protein
PREDICTED: Rattus norvegicus ER membrane protein complex subunit 4 (Emc4), trans...
PREDICTED: Rattus norvegicus ER membrane protein complex subunit 4 (Emc4), transcript variant X1, mRNA
gi|2678927969|ref|XM_063283315.1|

Nucleotide
ral guanine nucleotide dissociation stimulator, isoform CRA_a [Rattus norvegicus...
ral guanine nucleotide dissociation stimulator, isoform CRA_a [Rattus norvegicus]
gi|149039190|gb|EDL93410.1||gnl|WGS |rCP24886

Protein
UNVERIFIED: Phlegmacium georgiolens voucher GS03-1 RNA polymerase II largest sub...
UNVERIFIED: Phlegmacium georgiolens voucher GS03-1 RNA polymerase II largest subunit-like (rpb1) gene, partial sequence
gi|1707435561|gb|MK340961.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000182394	ISCA site 2 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic (Feb 4, 2013)	maternal	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

SCV000182394

ISCA site 2

See additional submitters

no assertion criteria provided

Pathogenic
(Feb 4, 2013)

maternal

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	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 2, SCV000182394.3

#	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	maternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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