GRCh38/hg38 16p11.2(chr16:29645363-30183432)x3 AND See cases

Clinical significance:Pathogenic (Last evaluated: Feb 5, 2018)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for GRCh38/hg38 16p11.2(chr16:29645363-30183432)x3]

GRCh38/hg38 16p11.2(chr16:29645363-30183432)x3

  • CDIPTOSP:CDIP transferase opposite strand, pseudogene [Gene - HGNC]
  • CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
  • HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
  • INO80E:INO80 complex subunit E [Gene - HGNC]
  • MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
  • PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
  • LOC112352679:Sharpr-MPRA regulatory region 12377 [Gene]
  • LOC112352680:Sharpr-MPRA regulatory region 6067 [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]
  • 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 - 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]
  • 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 - HGNC]
  • LOC101928595:uncharacterized LOC101928595 [Gene]
  • LOC112694756:uncharaterized LOC112694756 [Gene]
  • YPEL3:yippee like 3 [Gene - OMIM - HGNC]
  • ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
Genomic location:
Preferred name:
GRCh38/hg38 16p11.2(chr16:29645363-30183432)x3
  • NC_000016.10:g.(?_29645363)_(30183432_?)dup
  • NC_000016.8:g.(?_29564185)_(30102254_?)dup
  • NC_000016.9:g.(?_29656684)_(30194753_?)dup
dbVar: nssv579339; dbVar: nsv532931


See cases [See the Variation display for details]

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000081630ISCA site 6no assertion criteria providedPathogenic
(Feb 5, 2018)
not providedclinical testing

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


Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations. Clinical assertions have been curated as described in Kaminsky et al. 2011.


Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations. Clinical assertions have been curated as described in [Kaminsky, et al. 2011|/pubmed/21844811]. For additional ClinGen data, please see [nstd37|/dbvar/studies/nstd37/].


Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical testing



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]

Details of each submission

From ISCA site 6, SCV000081630.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)


16p11.2 recurrent region (includes TBX6) (proximal region) (BP4-BP5) (hg19 chr16: 29,649,996-30,199,855), enriched in cases with ID/DD, MCA etc vs controls, ClinGen triplosensitivity score = 3

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Nov 20, 2019

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