GRCh37/hg19 17p13.3(chr17:1-2538512)x4,5 AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 1, 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:: RCV000754117.1

Allele description [Variation Report for GRCh37/hg19 17p13.3(chr17:1-2538512)x4,5]

GRCh37/hg19 17p13.3(chr17:1-2538512)x4,5

Genes:

ABR:ABR activator of RhoGEF and GTPase [Gene - OMIM - HGNC]
CRK:CRK proto-oncogene, adaptor protein [Gene - OMIM - HGNC]
HIC1:HIC ZBTB transcriptional repressor 1 [Gene - OMIM - HGNC]
MNT:MAX network transcriptional repressor [Gene - OMIM - HGNC]
OVCA2:OVCA2 serine hydrolase domain containing [Gene - OMIM - HGNC]
RILP:Rab interacting lysosomal protein [Gene - OMIM - HGNC]
SMYD4:SET and MYND domain containing 4 [Gene - OMIM - HGNC]
SMG6:SMG6 nonsense mediated mRNA decay factor [Gene - OMIM - HGNC]
TLCD2:TLC domain containing 2 [Gene - HGNC]
TLCD3A:TLC domain containing 3A [Gene - OMIM - HGNC]
TSR1:TSR1 ribosome maturation factor [Gene - OMIM - HGNC]
VPS53:VPS53 subunit of GARP complex [Gene - OMIM - HGNC]
WDR81:WD repeat domain 81 [Gene - OMIM - HGNC]
BHLHA9:basic helix-loop-helix family member a9 [Gene - OMIM - HGNC]
DPH1:diphthamide biosynthesis 1 [Gene - OMIM - HGNC]
DOC2B:double C2 domain beta [Gene - OMIM - HGNC]
GEMIN4:gem nuclear organelle associated protein 4 [Gene - OMIM - HGNC]
GLOD4:glyoxalase domain containing 4 [Gene - HGNC]
INPP5K:inositol polyphosphate-5-phosphatase K [Gene - OMIM - HGNC]
LIAT1:ligand of ATE1 [Gene - HGNC]
METTL16:methyltransferase 16, RNA N6-adenosine [Gene - HGNC]
MIR132:microRNA 132 [Gene - OMIM - HGNC]
MIR212:microRNA 212 [Gene - OMIM - HGNC]
MIR22:microRNA 22 [Gene - OMIM - HGNC]
MRM3:mitochondrial rRNA methyltransferase 3 [Gene - OMIM - HGNC]
MYO1C:myosin IC [Gene - OMIM - HGNC]
NXN:nucleoredoxin [Gene - OMIM - HGNC]
PITPNA:phosphatidylinositol transfer protein alpha [Gene - OMIM - HGNC]
PAFAH1B1:platelet activating factor acetylhydrolase 1b regulatory subunit 1 [Gene - OMIM - HGNC]
PRPF8:pre-mRNA processing factor 8 [Gene - OMIM - HGNC]
RPH3AL:rabphilin 3A like (without C2 domains) [Gene - OMIM - HGNC]
RFLNB:refilin B [Gene - OMIM - HGNC]
RPA1:replication protein A1 [Gene - OMIM - HGNC]
RTN4RL1:reticulon 4 receptor like 1 [Gene - OMIM - HGNC]
SCARF1:scavenger receptor class F member 1 [Gene - OMIM - HGNC]
SRR:serine racemase [Gene - OMIM - HGNC]
SERPINF1:serpin family F member 1 [Gene - OMIM - HGNC]
SERPINF2:serpin family F member 2 [Gene - OMIM - HGNC]
SGSM2:small G protein signaling modulator 2 [Gene - OMIM - HGNC]
SLC43A2:solute carrier family 43 member 2 [Gene - OMIM - HGNC]
TRARG1:trafficking regulator of GLUT4 (SLC2A4) 1 [Gene - OMIM - HGNC]
TIMM22:translocase of inner mitochondrial membrane 22 [Gene - OMIM - HGNC]
YWHAE:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

17p13.3

Genomic location:

Chr17: 1 - 2538512 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 17p13.3(chr17:1-2538512)x4,5

Other names:

17p13.3(1-2538512)x4,5; 17p13.3(525-2529405)x4,5

HGVS:

Observations:

Condition(s)

Name:: Partial agenesis of the corpus callosum (PACC)
Synonyms:: Partial agenesis of corpus callosum; Severe intellectual retardation and intractable seizures
Identifiers:: MedGen: C0431368; Human Phenotype Ontology: HP:0001338

Name:: Ventriculomegaly
Identifiers:: MedGen: C3278923; Human Phenotype Ontology: HP:0002119

Name:: Echogenic fetal bowel
Identifiers:: MedGen: C2936423; Human Phenotype Ontology: HP:0010943

Name:: Bilateral fetal pyelectasis
Identifiers:: MedGen: C4023523; Human Phenotype Ontology: HP:0011129

Name:: Neurodevelopmental abnormality
Identifiers:: MedGen: C4022737; Human Phenotype Ontology: HP:0012759

Recent activity

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peptidylglycine alpha-amidating monooxygenase, isoform CRA_f [Rattus norvegicus]
peptidylglycine alpha-amidating monooxygenase, isoform CRA_f [Rattus norvegicus]
gi|149037444|gb|EDL91875.1||gnl|WGS |rCP24336

Protein
Chain A, GTP CYCLOHYDROLASE I
Chain A, GTP CYCLOHYDROLASE I
gi|5107437|pdb|1A9C|A

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000747897	Department of Obstetrics and Gynecology, Montefiore Medical Center	no assertion criteria provided	Uncertain significance (Apr 1, 2018)	unknown	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

SCV000747897

Department of Obstetrics and Gynecology, Montefiore Medical Center

no assertion criteria provided

Uncertain significance
(Apr 1, 2018)

unknown

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	unknown	yes	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

17p13.3 quadruplication: a prenatal and postpartum clinical characterization of a copy number variant.

Farris N, Wu H, Said-Delgado S, Suskin B, Klugman S.

Cold Spring Harb Mol Case Stud. 2018 Jun 1;4(3). doi:pii: a002196. 10.1101/mcs.a002196. Print 2018 Jun.

PubMed [citation]

PMID:: 29858378
PMCID:: PMC5983170

Details of each submission

From Department of Obstetrics and Gynecology, Montefiore Medical Center, SCV000747897.1

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

Description

Quadruplication of unknown significance, not previously reported at the site of a known duplication site; new pathogenic variant vs dose dependent phenotype.

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

Last Updated: Oct 14, 2023

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