Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 1, 2023
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:: RCV003448664.1

Allele description [Variation Report for Single allele]

Genes:

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]
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 - 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]
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]
YPEL3:yippee like 3 [Gene - OMIM - HGNC]
ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p11.2

Genomic location:

Chr16: 29651786 - 30199024 (on Assembly GRCh37)

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176306	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020)	Pathogenic (May 1, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176306

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)

Pathogenic
(May 1, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004176306.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This CNV is a 547 kb duplication of 16p11.2 on chromosome 16, (seq[GRCh37]dup(16)(p11.2);NC_000016.9:g.29651786_30199024dup), which is inherited. This CNV affects 27 protein-coding genes and is consistent with the proximal 16p11.2 recurrent region, which is subject to recurrent copy number changes due to the presence of a cluster of low copy repeats (PMID: 20301775). These recurrent breakpoints are sometimes referred to as BP4 and BP5. A few similar duplications have been observed in controls, consistent with the incomplete penetrance and variable phenotypes associated with 16p11.2 duplication (PMID: 21841781). Based on the available evidence, this CNV is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 17, 2023

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