GRCh38/hg38 15q26.1(chr15:92170113-93438995)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:: RCV000053225.4

Allele description [Variation Report for GRCh38/hg38 15q26.1(chr15:92170113-93438995)x1]

GRCh38/hg38 15q26.1(chr15:92170113-93438995)x1

Genes:

LOC130057963:ATAC-STARR-seq lymphoblastoid active region 10112 [Gene]
LOC130057964:ATAC-STARR-seq lymphoblastoid active region 10113 [Gene]
LOC130057965:ATAC-STARR-seq lymphoblastoid active region 10114 [Gene]
LOC130057970:ATAC-STARR-seq lymphoblastoid active region 10116 [Gene]
LOC130057971:ATAC-STARR-seq lymphoblastoid active region 10117 [Gene]
LOC130057974:ATAC-STARR-seq lymphoblastoid active region 10118 [Gene]
LOC130057975:ATAC-STARR-seq lymphoblastoid active region 10120 [Gene]
LOC130057976:ATAC-STARR-seq lymphoblastoid active region 10121 [Gene]
LOC130057977:ATAC-STARR-seq lymphoblastoid active region 10122 [Gene]
LOC130057978:ATAC-STARR-seq lymphoblastoid active region 10123 [Gene]
LOC130057979:ATAC-STARR-seq lymphoblastoid active region 10124 [Gene]
LOC130057980:ATAC-STARR-seq lymphoblastoid active region 10125 [Gene]
LOC130057981:ATAC-STARR-seq lymphoblastoid active region 10126 [Gene]
LOC130057982:ATAC-STARR-seq lymphoblastoid active region 10127 [Gene]
LOC130057985:ATAC-STARR-seq lymphoblastoid active region 10128 [Gene]
LOC130057986:ATAC-STARR-seq lymphoblastoid active region 10129 [Gene]
LOC130057987:ATAC-STARR-seq lymphoblastoid active region 10132 [Gene]
LOC130057988:ATAC-STARR-seq lymphoblastoid active region 10133 [Gene]
LOC130057966:ATAC-STARR-seq lymphoblastoid silent region 6840 [Gene]
LOC130057967:ATAC-STARR-seq lymphoblastoid silent region 6841 [Gene]
LOC130057968:ATAC-STARR-seq lymphoblastoid silent region 6842 [Gene]
LOC130057969:ATAC-STARR-seq lymphoblastoid silent region 6843 [Gene]
LOC130057972:ATAC-STARR-seq lymphoblastoid silent region 6844 [Gene]
LOC130057973:ATAC-STARR-seq lymphoblastoid silent region 6845 [Gene]
LOC130057983:ATAC-STARR-seq lymphoblastoid silent region 6848 [Gene]
LOC130057984:ATAC-STARR-seq lymphoblastoid silent region 6849 [Gene]
CHASERR:CHD2 adjacent suppressive regulatory RNA [Gene - HGNC]
LOC108251791:FAM174B-LINC01578 intergenic CAGE-defined high expression enhancer [Gene]
LOC126862226:MED14-independent group 3 enhancer GRCh37_chr15:92972458-92973657 [Gene]
LOC126862227:MED14-independent group 3 enhancer GRCh37_chr15:93447162-93448361 [Gene]
LOC126862229:MED14-independent group 3 enhancer GRCh37_chr15:93492919-93494118 [Gene]
LOC129390736:MPRA-validated peak2428 silencer [Gene]
LOC129390737:MPRA-validated peak2429 silencer [Gene]
LOC132090365:Neanderthal introgressed variant-containing enhancer experimental_42675 [Gene]
LOC132090366:Neanderthal introgressed variant-containing enhancer experimental_42698 [Gene]
LOC126862228:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93464712-93465911 [Gene]
LOC126862230:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93523977-93525176 [Gene]
ST8SIA2:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 [Gene - OMIM - HGNC]
LOC112296176:Sharpr-MPRA regulatory region 10912 [Gene]
LOC125146357:Sharpr-MPRA regulatory region 7580 [Gene]
CHD2:chromodomain helicase DNA binding protein 2 [Gene - OMIM - HGNC]
C15orf32:chromosome 15 putative open reading frame 32 [Gene - HGNC]
FAM174B:family with sequence similarity 174 member B [Gene - HGNC]
LINC00930:long intergenic non-protein coding RNA 930 [Gene - HGNC]
MIR3175:microRNA 3175 [Gene - HGNC]
PIRC76:piwi-interacting RNA cluster 76 [Gene - HGNC]
LOC105370980:putative uncharacterized protein UNQ9370/PRO34162 [Gene]
RGMA:repulsive guidance molecule BMP co-receptor a [Gene - OMIM - HGNC]
SLCO3A1:solute carrier organic anion transporter family member 3A1 [Gene - OMIM - HGNC]
LOC104613533:uncharacterized LOC104613533 [Gene]

Variant type:

copy number loss

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

GRCh38/hg38 15q26.1(chr15:92170113-93438995)x1

HGVS:

NC_000015.10:g.(?_92170113)_(93438995_?)del
NC_000015.8:g.(?_90514347)_(91783228_?)del
NC_000015.9:g.(?_92713343)_(93982224_?)del

Links:

dbVar: nssv577517; dbVar: nsv531905

Observations:

Condition(s)

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

Recent activity

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Homo sapiens parathyroid hormone 2 receptor (PTH2R), transcript variant 2, mRNA
Homo sapiens parathyroid hormone 2 receptor (PTH2R), transcript variant 2, mRNA
gi|1677530829|ref|NM_001309516.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000080583	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	not provided	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

SCV000080583

GeneDx

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

not provided

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	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, SCV000080583.4

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

Last Updated: Oct 14, 2023

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