GRCh38/hg38 16p11.2(chr16:29579233-30186020)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 14, 2018
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:: RCV000138443.7

Allele description [Variation Report for GRCh38/hg38 16p11.2(chr16:29579233-30186020)x1]

GRCh38/hg38 16p11.2(chr16:29579233-30186020)x1

Genes:

LOC130058757:ATAC-STARR-seq lymphoblastoid active region 10657 [Gene]
LOC130058760:ATAC-STARR-seq lymphoblastoid active region 10658 [Gene]
LOC130058761:ATAC-STARR-seq lymphoblastoid active region 10659 [Gene]
LOC130058762:ATAC-STARR-seq lymphoblastoid active region 10660 [Gene]
LOC130058763:ATAC-STARR-seq lymphoblastoid active region 10661 [Gene]
LOC130058764:ATAC-STARR-seq lymphoblastoid active region 10662 [Gene]
LOC130058765:ATAC-STARR-seq lymphoblastoid active region 10663 [Gene]
LOC130058766:ATAC-STARR-seq lymphoblastoid active region 10664 [Gene]
LOC130058769:ATAC-STARR-seq lymphoblastoid active region 10665 [Gene]
LOC130058770:ATAC-STARR-seq lymphoblastoid active region 10667 [Gene]
LOC130058772:ATAC-STARR-seq lymphoblastoid active region 10668 [Gene]
LOC130058773:ATAC-STARR-seq lymphoblastoid active region 10669 [Gene]
LOC130058774:ATAC-STARR-seq lymphoblastoid active region 10670 [Gene]
LOC130058775:ATAC-STARR-seq lymphoblastoid active region 10671 [Gene]
LOC130058777:ATAC-STARR-seq lymphoblastoid active region 10672 [Gene]
LOC130058778:ATAC-STARR-seq lymphoblastoid active region 10673 [Gene]
LOC130058780:ATAC-STARR-seq lymphoblastoid active region 10674 [Gene]
LOC130058781:ATAC-STARR-seq lymphoblastoid active region 10675 [Gene]
LOC130058783:ATAC-STARR-seq lymphoblastoid active region 10676 [Gene]
LOC130058787:ATAC-STARR-seq lymphoblastoid active region 10677 [Gene]
LOC130058790:ATAC-STARR-seq lymphoblastoid active region 10679 [Gene]
LOC130058792:ATAC-STARR-seq lymphoblastoid active region 10680 [Gene]
LOC130058793:ATAC-STARR-seq lymphoblastoid active region 10682 [Gene]
LOC130058794:ATAC-STARR-seq lymphoblastoid active region 10683 [Gene]
LOC130058799:ATAC-STARR-seq lymphoblastoid active region 10684 [Gene]
LOC130058802:ATAC-STARR-seq lymphoblastoid active region 10686 [Gene]
LOC130058803:ATAC-STARR-seq lymphoblastoid active region 10687 [Gene]
LOC130058808:ATAC-STARR-seq lymphoblastoid active region 10688 [Gene]
LOC130058810:ATAC-STARR-seq lymphoblastoid active region 10689 [Gene]
LOC130058812:ATAC-STARR-seq lymphoblastoid active region 10690 [Gene]
LOC130058814:ATAC-STARR-seq lymphoblastoid active region 10691 [Gene]
LOC130058815:ATAC-STARR-seq lymphoblastoid active region 10692 [Gene]
LOC130058816:ATAC-STARR-seq lymphoblastoid active region 10693 [Gene]
LOC130058756:ATAC-STARR-seq lymphoblastoid silent region 7326 [Gene]
LOC130058758:ATAC-STARR-seq lymphoblastoid silent region 7327 [Gene]
LOC130058759:ATAC-STARR-seq lymphoblastoid silent region 7328 [Gene]
LOC130058767:ATAC-STARR-seq lymphoblastoid silent region 7329 [Gene]
LOC130058768:ATAC-STARR-seq lymphoblastoid silent region 7330 [Gene]
LOC130058771:ATAC-STARR-seq lymphoblastoid silent region 7331 [Gene]
LOC130058776:ATAC-STARR-seq lymphoblastoid silent region 7332 [Gene]
LOC130058779:ATAC-STARR-seq lymphoblastoid silent region 7333 [Gene]
LOC130058782:ATAC-STARR-seq lymphoblastoid silent region 7334 [Gene]
LOC130058784:ATAC-STARR-seq lymphoblastoid silent region 7335 [Gene]
LOC130058785:ATAC-STARR-seq lymphoblastoid silent region 7336 [Gene]
LOC130058786:ATAC-STARR-seq lymphoblastoid silent region 7337 [Gene]
LOC130058788:ATAC-STARR-seq lymphoblastoid silent region 7338 [Gene]
LOC130058789:ATAC-STARR-seq lymphoblastoid silent region 7339 [Gene]
LOC130058791:ATAC-STARR-seq lymphoblastoid silent region 7340 [Gene]
LOC130058795:ATAC-STARR-seq lymphoblastoid silent region 7341 [Gene]
LOC130058796:ATAC-STARR-seq lymphoblastoid silent region 7342 [Gene]
LOC130058797:ATAC-STARR-seq lymphoblastoid silent region 7343 [Gene]
LOC130058798:ATAC-STARR-seq lymphoblastoid silent region 7344 [Gene]
LOC130058800:ATAC-STARR-seq lymphoblastoid silent region 7345 [Gene]
LOC130058801:ATAC-STARR-seq lymphoblastoid silent region 7346 [Gene]
LOC130058804:ATAC-STARR-seq lymphoblastoid silent region 7347 [Gene]
LOC130058805:ATAC-STARR-seq lymphoblastoid silent region 7348 [Gene]
LOC130058806:ATAC-STARR-seq lymphoblastoid silent region 7349 [Gene]
LOC130058807:ATAC-STARR-seq lymphoblastoid silent region 7350 [Gene]
LOC130058809:ATAC-STARR-seq lymphoblastoid silent region 7351 [Gene]
LOC130058811:ATAC-STARR-seq lymphoblastoid silent region 7352 [Gene]
LOC130058813:ATAC-STARR-seq lymphoblastoid silent region 7356 [Gene]
LOC130058817:ATAC-STARR-seq lymphoblastoid silent region 7357 [Gene]
LOC130058818:ATAC-STARR-seq lymphoblastoid silent region 7358 [Gene]
CDIPTOSP:CDIP transferase opposite strand, pseudogene [Gene - HGNC]
CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
CORO1A-AS1:CORO1A antisense RNA 1 [Gene - HGNC]
LOC116276452:CRISPRi-validated cis-regulatory element chr16.2261 [Gene]
HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
INO80E:INO80 complex subunit E [Gene - HGNC]
LOC129390783:MPRA-validated peak2562 silencer [Gene]
MVP-DT:MVP divergent transcript [Gene - HGNC]
MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
LOC125146440:Sharpr-MPRA regulatory region 10200 [Gene]
LOC125146439:Sharpr-MPRA regulatory region 12104 [Gene]
LOC112352679:Sharpr-MPRA regulatory region 12377 [Gene]
LOC121847977:Sharpr-MPRA regulatory region 13449 [Gene]
LOC121847976:Sharpr-MPRA regulatory region 1439 [Gene]
LOC112352680:Sharpr-MPRA regulatory region 6067 [Gene]
LOC121587540:Sharpr-MPRA regulatory region 8247 [Gene]
LOC125146441:Sharpr-MPRA regulatory region 9068 [Gene]
TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
TAOK2:TAO kinase 2 [Gene - OMIM - HGNC]
TLCD3B:TLC domain containing 3B [Gene - OMIM - HGNC]
YPEL3-DT:YPEL3 divergent transcript [Gene - HGNC]
ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
ASPHD1:aspartate beta-hydroxylase domain containing 1 [Gene - HGNC]
C16orf54:chromosome 16 open reading frame 54 [Gene - HGNC]
C16orf92:chromosome 16 open reading frame 92 [Gene - OMIM - HGNC]
CORO1A:coronin 1A [Gene - OMIM - HGNC]
DOC2A:double C2 domain alpha [Gene - OMIM - HGNC]
GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
KIF22:kinesin family member 22 [Gene - OMIM - HGNC]
MVP:major vault protein [Gene - OMIM - HGNC]
MIR3680-2:microRNA 3680-2 [Gene - HGNC]
MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
KCTD13:potassium channel tetramerization domain containing 13 [Gene - OMIM - HGNC]
PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
QPRT:quinolinate phosphoribosyltransferase [Gene - OMIM - HGNC]
SEZ6L2:seizure related 6 homolog like 2 [Gene - OMIM - HGNC]
SPN:sialophorin [Gene - OMIM - HGNC]
TMEM219:transmembrane protein 219 [Gene - OMIM - HGNC]
LOC112694756:uncharaterized LOC112694756 [Gene]
YPEL3:yippee like 3 [Gene - OMIM - HGNC]
ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

GRCh38/hg38 16p11.2(chr16:29579233-30186020)x1

HGVS:

NC_000016.10:g.(?_29579233)_(30186020_?)del
NC_000016.8:g.(?_29498055)_(30104842_?)del
NC_000016.9:g.(?_29590554)_(30197341_?)del

Links:

dbVar: nssv14081976; dbVar: nssv1415102; dbVar: nssv1415349; dbVar: nssv1495013; dbVar: nssv1495017; dbVar: nssv1495022; dbVar: nssv1603183; dbVar: nssv1604378; dbVar: nssv1608182; dbVar: nssv1608844; dbVar: nssv1608929; dbVar: nssv1609606; dbVar: nssv1610093; dbVar: nssv3396548; dbVar: nsv915682

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
SCV000178771	ISCA site 1	no assertion criteria provided	Pathogenic (Feb 14, 2018)	unknown, 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

SCV000178771

ISCA site 1

no assertion criteria provided

Pathogenic
(Feb 14, 2018)

unknown, 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	2	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	yes	10	not provided	not provided	not provided	not provided	clinical testing
human	not provided	yes	2	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 1, SCV000178771.6

#	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)
3	not provided	1	not provided	not provided	clinical testing	PubMed (1)
4	not provided	1	not provided	not provided	clinical testing	PubMed (1)
5	not provided	1	not provided	not provided	clinical testing	PubMed (1)
6	not provided	1	not provided	not provided	clinical testing	PubMed (1)
7	not provided	1	not provided	not provided	clinical testing	PubMed (1)
8	not provided	1	not provided	not provided	clinical testing	PubMed (1)
9	not provided	1	not provided	not provided	clinical testing	PubMed (1)
10	not provided	1	not provided	not provided	clinical testing	PubMed (1)
11	not provided	1	not provided	not provided	clinical testing	PubMed (1)
12	not provided	1	not provided	not provided	clinical testing	PubMed (1)
13	human	1	not provided	not provided	clinical testing	PubMed (1)
14	human	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
3	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
4	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
5	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
6	maternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
7	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
8	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
9	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
10	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
11	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
12	maternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
13	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
14	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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