GRCh38/hg38 15q13.2-13.3(chr15:30662523-32217725)x1 AND See cases

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 12, 2011
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000148066.4

Allele description [Variation Report for GRCh38/hg38 15q13.2-13.3(chr15:30662523-32217725)x1]

GRCh38/hg38 15q13.2-13.3(chr15:30662523-32217725)x1

Genes:

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]
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]
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]
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]
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(chr15:30662523-32217725)x1

HGVS:

NC_000015.10:g.(?_30662523)_(32217725_?)del
NC_000015.8:g.(?_28742018)_(30297218_?)del
NC_000015.9:g.(?_30954726)_(32509926_?)del

Links:

dbVar: nssv579752; dbVar: nssv579758; dbVar: nssv579761; dbVar: nsv1067611

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
SCV000190741	ISCA site 17 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000190742	ISCA site 4 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	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

SCV000190741

ISCA site 17

See additional submitters

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

unknown

clinical testing

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

SCV000190742

ISCA site 4

See additional submitters

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
not provided	not provided	yes	2	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 ISCA site 17, SCV000190741.2

#	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)

#	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

From ISCA site 4, SCV000190742.2

#	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: May 7, 2024

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