GRCh38/hg38 16q12.1-12.2(chr16:47250644-54121476)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:: RCV000053329.5

Allele description [Variation Report for GRCh38/hg38 16q12.1-12.2(chr16:47250644-54121476)x1]

GRCh38/hg38 16q12.1-12.2(chr16:47250644-54121476)x1

Genes:

AKTIP:AKT interacting protein [Gene - OMIM - HGNC]
LOC130058948:ATAC-STARR-seq lymphoblastoid active region 10786 [Gene]
LOC130058949:ATAC-STARR-seq lymphoblastoid active region 10787 [Gene]
LOC130058950:ATAC-STARR-seq lymphoblastoid active region 10788 [Gene]
LOC130058951:ATAC-STARR-seq lymphoblastoid active region 10789 [Gene]
LOC130058953:ATAC-STARR-seq lymphoblastoid active region 10791 [Gene]
LOC130058957:ATAC-STARR-seq lymphoblastoid active region 10792 [Gene]
LOC130058958:ATAC-STARR-seq lymphoblastoid active region 10793 [Gene]
LOC130058959:ATAC-STARR-seq lymphoblastoid active region 10795 [Gene]
LOC130058960:ATAC-STARR-seq lymphoblastoid active region 10796 [Gene]
LOC130058961:ATAC-STARR-seq lymphoblastoid active region 10797 [Gene]
LOC130058962:ATAC-STARR-seq lymphoblastoid active region 10798 [Gene]
LOC130058964:ATAC-STARR-seq lymphoblastoid active region 10799 [Gene]
LOC130058965:ATAC-STARR-seq lymphoblastoid active region 10800 [Gene]
LOC130058966:ATAC-STARR-seq lymphoblastoid active region 10801 [Gene]
LOC130058968:ATAC-STARR-seq lymphoblastoid active region 10802 [Gene]
LOC130058972:ATAC-STARR-seq lymphoblastoid active region 10804 [Gene]
LOC130058973:ATAC-STARR-seq lymphoblastoid active region 10805 [Gene]
LOC130058974:ATAC-STARR-seq lymphoblastoid active region 10807 [Gene]
LOC130058986:ATAC-STARR-seq lymphoblastoid active region 10808 [Gene]
LOC130058987:ATAC-STARR-seq lymphoblastoid active region 10809 [Gene]
LOC130058988:ATAC-STARR-seq lymphoblastoid active region 10810 [Gene]
LOC130058990:ATAC-STARR-seq lymphoblastoid active region 10811 [Gene]
LOC130058991:ATAC-STARR-seq lymphoblastoid active region 10812 [Gene]
LOC130058992:ATAC-STARR-seq lymphoblastoid active region 10814 [Gene]
LOC130058993:ATAC-STARR-seq lymphoblastoid active region 10815 [Gene]
LOC130058994:ATAC-STARR-seq lymphoblastoid active region 10816 [Gene]
LOC130058997:ATAC-STARR-seq lymphoblastoid active region 10817 [Gene]
LOC130059001:ATAC-STARR-seq lymphoblastoid active region 10818 [Gene]
LOC130059004:ATAC-STARR-seq lymphoblastoid active region 10819 [Gene]
LOC130059005:ATAC-STARR-seq lymphoblastoid active region 10820 [Gene]
LOC130059006:ATAC-STARR-seq lymphoblastoid active region 10821 [Gene]
LOC130059008:ATAC-STARR-seq lymphoblastoid active region 10822 [Gene]
LOC130059009:ATAC-STARR-seq lymphoblastoid active region 10823 [Gene]
LOC130059010:ATAC-STARR-seq lymphoblastoid active region 10824 [Gene]
LOC130059011:ATAC-STARR-seq lymphoblastoid active region 10825 [Gene]
LOC130059013:ATAC-STARR-seq lymphoblastoid active region 10826 [Gene]
LOC130059014:ATAC-STARR-seq lymphoblastoid active region 10827 [Gene]
LOC130059016:ATAC-STARR-seq lymphoblastoid active region 10828 [Gene]
LOC130059018:ATAC-STARR-seq lymphoblastoid active region 10831 [Gene]
LOC130059019:ATAC-STARR-seq lymphoblastoid active region 10832 [Gene]
LOC130059020:ATAC-STARR-seq lymphoblastoid active region 10833 [Gene]
LOC130059021:ATAC-STARR-seq lymphoblastoid active region 10834 [Gene]
LOC130059022:ATAC-STARR-seq lymphoblastoid active region 10835 [Gene]
LOC130059023:ATAC-STARR-seq lymphoblastoid active region 10836 [Gene]
LOC130059024:ATAC-STARR-seq lymphoblastoid active region 10840 [Gene]
LOC130059025:ATAC-STARR-seq lymphoblastoid active region 10841 [Gene]
LOC130059029:ATAC-STARR-seq lymphoblastoid active region 10842 [Gene]
LOC130059030:ATAC-STARR-seq lymphoblastoid active region 10843 [Gene]
LOC130059032:ATAC-STARR-seq lymphoblastoid active region 10844 [Gene]
LOC130059033:ATAC-STARR-seq lymphoblastoid active region 10845 [Gene]
LOC130059034:ATAC-STARR-seq lymphoblastoid active region 10846 [Gene]
LOC130058947:ATAC-STARR-seq lymphoblastoid silent region 7451 [Gene]
LOC130058952:ATAC-STARR-seq lymphoblastoid silent region 7452 [Gene]
LOC130058954:ATAC-STARR-seq lymphoblastoid silent region 7454 [Gene]
LOC130058955:ATAC-STARR-seq lymphoblastoid silent region 7455 [Gene]
LOC130058956:ATAC-STARR-seq lymphoblastoid silent region 7456 [Gene]
LOC130058963:ATAC-STARR-seq lymphoblastoid silent region 7457 [Gene]
LOC130058967:ATAC-STARR-seq lymphoblastoid silent region 7458 [Gene]
LOC130058969:ATAC-STARR-seq lymphoblastoid silent region 7459 [Gene]
LOC130058970:ATAC-STARR-seq lymphoblastoid silent region 7460 [Gene]
LOC130058971:ATAC-STARR-seq lymphoblastoid silent region 7461 [Gene]
LOC130058975:ATAC-STARR-seq lymphoblastoid silent region 7462 [Gene]
LOC130058976:ATAC-STARR-seq lymphoblastoid silent region 7463 [Gene]
LOC130058977:ATAC-STARR-seq lymphoblastoid silent region 7464 [Gene]
LOC130058978:ATAC-STARR-seq lymphoblastoid silent region 7465 [Gene]
LOC130058979:ATAC-STARR-seq lymphoblastoid silent region 7468 [Gene]
LOC130058980:ATAC-STARR-seq lymphoblastoid silent region 7469 [Gene]
LOC130058981:ATAC-STARR-seq lymphoblastoid silent region 7470 [Gene]
LOC130058982:ATAC-STARR-seq lymphoblastoid silent region 7471 [Gene]
LOC130058983:ATAC-STARR-seq lymphoblastoid silent region 7475 [Gene]
LOC130058984:ATAC-STARR-seq lymphoblastoid silent region 7476 [Gene]
LOC130058985:ATAC-STARR-seq lymphoblastoid silent region 7477 [Gene]
LOC130058989:ATAC-STARR-seq lymphoblastoid silent region 7478 [Gene]
LOC130058995:ATAC-STARR-seq lymphoblastoid silent region 7481 [Gene]
LOC130058996:ATAC-STARR-seq lymphoblastoid silent region 7482 [Gene]
LOC130058998:ATAC-STARR-seq lymphoblastoid silent region 7483 [Gene]
LOC130058999:ATAC-STARR-seq lymphoblastoid silent region 7484 [Gene]
LOC130059000:ATAC-STARR-seq lymphoblastoid silent region 7485 [Gene]
LOC130059002:ATAC-STARR-seq lymphoblastoid silent region 7486 [Gene]
LOC130059003:ATAC-STARR-seq lymphoblastoid silent region 7487 [Gene]
LOC130059007:ATAC-STARR-seq lymphoblastoid silent region 7489 [Gene]
LOC130059012:ATAC-STARR-seq lymphoblastoid silent region 7490 [Gene]
LOC130059015:ATAC-STARR-seq lymphoblastoid silent region 7491 [Gene]
LOC130059017:ATAC-STARR-seq lymphoblastoid silent region 7492 [Gene]
LOC130059026:ATAC-STARR-seq lymphoblastoid silent region 7494 [Gene]
LOC130059027:ATAC-STARR-seq lymphoblastoid silent region 7495 [Gene]
LOC130059028:ATAC-STARR-seq lymphoblastoid silent region 7496 [Gene]
LOC130059031:ATAC-STARR-seq lymphoblastoid silent region 7500 [Gene]
LOC130059035:ATAC-STARR-seq lymphoblastoid silent region 7502 [Gene]
ABCC11:ATP binding cassette subfamily C member 11 [Gene - OMIM - HGNC]
ABCC12:ATP binding cassette subfamily C member 12 [Gene - OMIM - HGNC]
LOC126862337:BRD4-independent group 4 enhancer GRCh37_chr16:47920785-47921984 [Gene]
LOC126862349:BRD4-independent group 4 enhancer GRCh37_chr16:52611160-52612359 [Gene]
LOC126862336:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:47767625-47768824 [Gene]
LOC126862340:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:48997204-48998403 [Gene]
LOC126862341:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:49681934-49683133 [Gene]
LOC126862343:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:50353005-50354204 [Gene]
LOC126862344:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:50430839-50432038 [Gene]
LOC126862345:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:51426797-51427996 [Gene]
LOC126862350:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:52662737-52663936 [Gene]
LOC126862351:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:52831610-52832809 [Gene]
CHD9NB:CHD9 neighbor [Gene - HGNC]
CNEP1R1:CTD nuclear envelope phosphatase 1 regulatory subunit 1 [Gene - OMIM - HGNC]
CYLD-AS1:CYLD antisense RNA 1 [Gene - HGNC]
CYLD-AS2:CYLD antisense RNA 2 [Gene - HGNC]
CYLD:CYLD lysine 63 deubiquitinase [Gene - OMIM - HGNC]
FTO:FTO alpha-ketoglutarate dependent dioxygenase [Gene - OMIM - HGNC]
FTO-IT1:FTO intronic transcript 1 [Gene - HGNC]
HEATR3:HEAT repeat containing 3 [Gene - OMIM - HGNC]
HEATR3-AS1:HEATR3 antisense RNA 1 [Gene - HGNC]
LOC126862342:MED14-independent group 3 enhancer GRCh37_chr16:50347343-50348542 [Gene]
LOC126862348:MED14-independent group 3 enhancer GRCh37_chr16:52331523-52332722 [Gene]
LOC126862354:MED14-independent group 3 enhancer GRCh37_chr16:53411888-53413087 [Gene]
LOC129390788:MPRA-validated peak2581 silencer [Gene]
LOC129390789:MPRA-validated peak2585 silencer [Gene]
LOC129390790:MPRA-validated peak2586 silencer [Gene]
LOC129390791:MPRA-validated peak2587 silencer [Gene]
LOC129390792:MPRA-validated peak2588 silencer [Gene]
LOC129390793:MPRA-validated peak2589 silencer [Gene]
LOC129390794:MPRA-validated peak2593 silencer [Gene]
LOC129390795:MPRA-validated peak2596 silencer [Gene]
N4BP1:NEDD4 binding protein 1 [Gene - OMIM - HGNC]
NKD1:NKD inhibitor of WNT signaling pathway 1 [Gene - OMIM - HGNC]
LOC132090379:Neanderthal introgressed variant-containing enhancer experimental_43383 [Gene]
LOC132090380:Neanderthal introgressed variant-containing enhancer experimental_43384 [Gene]
LOC126862338:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:48156892-48158091 [Gene]
LOC126862339:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:48191888-48193087 [Gene]
LOC126862346:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:51611051-51612250 [Gene]
LOC126862347:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:51654939-51656138 [Gene]
LOC126862352:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:52846552-52847751 [Gene]
LOC126862353:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:53132870-53134069 [Gene]
RBL2:RB transcriptional corepressor like 2 [Gene - OMIM - HGNC]
RPGRIP1L:RPGRIP1 like [Gene - OMIM - HGNC]
LOC112449716:Sharpr-MPRA regulatory region 10092 [Gene]
LOC112449713:Sharpr-MPRA regulatory region 10524 [Gene]
LOC121847988:Sharpr-MPRA regulatory region 10980 [Gene]
LOC125177307:Sharpr-MPRA regulatory region 11329 [Gene]
LOC125177309:Sharpr-MPRA regulatory region 1297 [Gene]
LOC113939954:Sharpr-MPRA regulatory region 13482 [Gene]
LOC112449714:Sharpr-MPRA regulatory region 13528 [Gene]
LOC125177308:Sharpr-MPRA regulatory region 14141 [Gene]
LOC125177305:Sharpr-MPRA regulatory region 14159 [Gene]
LOC113939953:Sharpr-MPRA regulatory region 1482 [Gene]
LOC125177304:Sharpr-MPRA regulatory region 15629 [Gene]
LOC113939952:Sharpr-MPRA regulatory region 1667 [Gene]
LOC121847987:Sharpr-MPRA regulatory region 2137 [Gene]
LOC125177313:Sharpr-MPRA regulatory region 2551 [Gene]
LOC125177312:Sharpr-MPRA regulatory region 3100 [Gene]
LOC125146444:Sharpr-MPRA regulatory region 3115 [Gene]
LOC121587545:Sharpr-MPRA regulatory region 4020 [Gene]
LOC112449715:Sharpr-MPRA regulatory region 4070 [Gene]
LOC112449717:Sharpr-MPRA regulatory region 7594 [Gene]
LOC125177306:Sharpr-MPRA regulatory region 8986 [Gene]
LOC125177311:Sharpr-MPRA regulatory region 9242 [Gene]
LOC125177302:Sharpr-MPRA regulatory region 9701 [Gene]
TOX3:TOX high mobility group box family member 3 [Gene - OMIM - HGNC]
LOC110120823:VISTA enhancer hs101 [Gene]
LOC110120826:VISTA enhancer hs124 [Gene]
LOC110121339:VISTA enhancer hs1300 [Gene]
LOC110120836:VISTA enhancer hs152 [Gene]
LOC110120837:VISTA enhancer hs155 [Gene]
LOC110120838:VISTA enhancer hs156 [Gene]
LOC110120839:VISTA enhancer hs157 [Gene]
LOC110120840:VISTA enhancer hs161 [Gene]
LOC110120841:VISTA enhancer hs162 [Gene]
LOC110120580:VISTA enhancer hs52 [Gene]
LOC110120581:VISTA enhancer hs59 [Gene]
LOC110120912:VISTA enhancer hs625 [Gene]
LOC110120582:VISTA enhancer hs65 [Gene]
LOC110120583:VISTA enhancer hs71 [Gene]
LOC110120584:VISTA enhancer hs72 [Gene]
LOC110120585:VISTA enhancer hs73 [Gene]
LOC110120586:VISTA enhancer hs74 [Gene]
LOC110120587:VISTA enhancer hs76 [Gene]
LOC110120588:VISTA enhancer hs79 [Gene]
LOC110120939:VISTA enhancer hs848 [Gene]
ADCY7:adenylate cyclase 7 [Gene - OMIM - HGNC]
BRD7:bromodomain containing 7 [Gene - OMIM - HGNC]
CASC16:cancer susceptibility 16 [Gene - HGNC]
CASC22:cancer susceptibility 22 [Gene - HGNC]
CBLN1:cerebellin 1 precursor [Gene - OMIM - HGNC]
CHD9:chromodomain helicase DNA binding protein 9 [Gene - OMIM - HGNC]
C16orf78:chromosome 16 open reading frame 78 [Gene - HGNC]
HNRNPA1L3:heterogeneous nuclear ribonucleoprotein A1 like 3 [Gene - HGNC]
ITFG1:integrin alpha FG-GAP repeat containing 1 [Gene - OMIM - HGNC]
LONP2:lon peptidase 2, peroxisomal [Gene - OMIM - HGNC]
LINC01571:long intergenic non-protein coding RNA 1571 [Gene - HGNC]
LINC02127:long intergenic non-protein coding RNA 2127 [Gene - HGNC]
LINC02128:long intergenic non-protein coding RNA 2128 [Gene - HGNC]
LINC02133:long intergenic non-protein coding RNA 2133 [Gene - HGNC]
LINC02134:long intergenic non-protein coding RNA 2134 [Gene - HGNC]
LINC02168:long intergenic non-protein coding RNA 2168 [Gene - HGNC]
LINC02178:long intergenic non-protein coding RNA 2178 [Gene - HGNC]
LINC02179:long intergenic non-protein coding RNA 2179 [Gene - HGNC]
LINC02180:long intergenic non-protein coding RNA 2180 [Gene - HGNC]
LINC02192:long intergenic non-protein coding RNA 2192 [Gene - HGNC]
LINC02911:long intergenic non-protein coding RNA 2911 [Gene - HGNC]
LINC03064:long intergenic non-protein coding RNA 3064 [Gene - HGNC]
LINC00919:long intergenic non-protein coding RNA 919 [Gene - HGNC]
MIR3181:microRNA 3181 [Gene - HGNC]
MIR6771:microRNA 6771 [Gene - HGNC]
NOD2:nucleotide binding oligomerization domain containing 2 [Gene - OMIM - HGNC]
PHKB:phosphorylase kinase regulatory subunit beta [Gene - OMIM - HGNC]
SIAH1:siah E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]
SNX20:sorting nexin 20 [Gene - OMIM - HGNC]
SALL1:spalt like transcription factor 1 [Gene - OMIM - HGNC]
TENT4B:terminal nucleotidyltransferase 4B [Gene - OMIM - HGNC]
LOC101927272:uncharacterized LOC101927272 [Gene]
LOC102723373:uncharacterized LOC102723373 [Gene]
LOC105371240:uncharacterized LOC105371240 [Gene]
ZNF423:zinc finger protein 423 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

16q12.1-12.2

Genomic location:

Preferred name:

GRCh38/hg38 16q12.1-12.2(chr16:47250644-54121476)x1

HGVS:

NC_000016.10:g.(?_47250644)_(54121476_?)del
NC_000016.8:g.(?_45842056)_(52712889_?)del
NC_000016.9:g.(?_47284555)_(54155388_?)del

Links:

dbVar: nssv577553; dbVar: nsv532010

Observations:

Condition(s)

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

Recent activity

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unnamed protein product [Homo sapiens]
unnamed protein product [Homo sapiens]
gi|194375872|dbj|BAG57280.1|

Protein
hCG2022032, isoform CRA_d [Homo sapiens]
hCG2022032, isoform CRA_d [Homo sapiens]
gi|119598682|gb|EAW78276.1||gnl|WGS |hCP1784601

Protein
Cylicin, basic protein of sperm head cytoskeleton 1 [Homo sapiens]
Cylicin, basic protein of sperm head cytoskeleton 1 [Homo sapiens]
gi|116496757|gb|AAI26462.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000080687	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

SCV000080687

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, SCV000080687.4

#	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

ClinVar

Relating variation to medicine