GRCh38/hg38 16p11.2(chr16:28710478-29025786)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:: RCV000053492.7

Allele description [Variation Report for GRCh38/hg38 16p11.2(chr16:28710478-29025786)x1]

GRCh38/hg38 16p11.2(chr16:28710478-29025786)x1

Genes:

LOC130058735:ATAC-STARR-seq lymphoblastoid active region 10645 [Gene]
LOC130058736:ATAC-STARR-seq lymphoblastoid active region 10646 [Gene]
LOC130058738:ATAC-STARR-seq lymphoblastoid active region 10648 [Gene]
LOC130058739:ATAC-STARR-seq lymphoblastoid active region 10649 [Gene]
LOC130058742:ATAC-STARR-seq lymphoblastoid active region 10650 [Gene]
LOC130058743:ATAC-STARR-seq lymphoblastoid active region 10651 [Gene]
LOC130058746:ATAC-STARR-seq lymphoblastoid active region 10652 [Gene]
LOC130058747:ATAC-STARR-seq lymphoblastoid active region 10653 [Gene]
LOC130058748:ATAC-STARR-seq lymphoblastoid active region 10654 [Gene]
LOC130058734:ATAC-STARR-seq lymphoblastoid silent region 7313 [Gene]
LOC130058737:ATAC-STARR-seq lymphoblastoid silent region 7314 [Gene]
LOC130058740:ATAC-STARR-seq lymphoblastoid silent region 7315 [Gene]
LOC130058741:ATAC-STARR-seq lymphoblastoid silent region 7316 [Gene]
LOC130058744:ATAC-STARR-seq lymphoblastoid silent region 7317 [Gene]
LOC130058745:ATAC-STARR-seq lymphoblastoid silent region 7318 [Gene]
LOC130058749:ATAC-STARR-seq lymphoblastoid silent region 7321 [Gene]
LOC130058750:ATAC-STARR-seq lymphoblastoid silent region 7322 [Gene]
LOC130058751:ATAC-STARR-seq lymphoblastoid silent region 7323 [Gene]
LOC130058752:ATAC-STARR-seq lymphoblastoid silent region 7324 [Gene]
ATP2A1-AS1:ATP2A1 antisense RNA 1 [Gene - HGNC]
ATP2A1:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Gene - OMIM - HGNC]
CD19:CD19 molecule [Gene - OMIM - HGNC]
LOC129390780:MPRA-validated peak2552 silencer [Gene]
LOC129390781:MPRA-validated peak2553 silencer [Gene]
NFATC2IP-AS1:NFATC2IP antisense RNA 1 [Gene - HGNC]
SH2B1:SH2B adaptor protein 1 [Gene - OMIM - HGNC]
SPNS1:SPNS lysolipid transporter 1, lysophospholipid [Gene - OMIM - HGNC]
LOC112340393:Sharpr-MPRA regulatory region 4004 [Gene]
TUFM:Tu translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
ATXN2L:ataxin 2 like [Gene - OMIM - HGNC]
EIF3C:eukaryotic translation initiation factor 3 subunit C [Gene - OMIM - HGNC]
LAT:linker for activation of T cells [Gene - OMIM - HGNC]
MIR4517:microRNA 4517 [Gene - HGNC]
MIR4721:microRNA 4721 [Gene - HGNC]
MIR6862-2:microRNA 6862-2 [Gene - HGNC]
NFATC2IP:nuclear factor of activated T cells 2 interacting protein [Gene - OMIM - HGNC]
NPIPB9:nuclear pore complex interacting protein family member B9 [Gene - HGNC]
RABEP2:rabaptin, RAB GTPase binding effector protein 2 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

GRCh38/hg38 16p11.2(chr16:28710478-29025786)x1

HGVS:

NC_000016.10:g.(?_28710478)_(29025786_?)del
NC_000016.8:g.(?_28629300)_(28944608_?)del
NC_000016.9:g.(?_28721799)_(29037107_?)del

Links:

dbVar: nssv577780; dbVar: nssv577891; dbVar: nsv532169

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
SCV000080850	ISCA Site 6 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	paternal, 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

SCV000080850

ISCA Site 6

See additional submitters

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

paternal, 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	paternal	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	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 ISCA Site 6, SCV000080850.5

#	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)

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

Last Updated: May 7, 2024

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