GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 1, 2018
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:: RCV000767704.1

Allele description [Variation Report for GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616)]

GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616)

Genes:

ALAS1:5'-aminolevulinate synthase 1 [Gene - OMIM - HGNC]
NT5DC2:5'-nucleotidase domain containing 2 [Gene - HGNC]
PFKFB4:6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 [Gene - OMIM - HGNC]
ALS2CL:ALS2 C-terminal like [Gene - OMIM - HGNC]
ARIH2OS:ARIH2 opposite strand lncRNA [Gene - HGNC]
ATRIP:ATR interacting protein [Gene - OMIM - HGNC]
BAP1:BRCA1 associated deubiquitinase 1 [Gene - OMIM - HGNC]
CCR1:C-C motif chemokine receptor 1 [Gene - OMIM - HGNC]
CCR2:C-C motif chemokine receptor 2 [Gene - OMIM - HGNC]
CCR3:C-C motif chemokine receptor 3 [Gene - OMIM - HGNC]
CCR5:C-C motif chemokine receptor 5 [Gene - OMIM - HGNC]
CCR9:C-C motif chemokine receptor 9 [Gene - OMIM - HGNC]
CCRL2:C-C motif chemokine receptor like 2 [Gene - OMIM - HGNC]
CXCR6:C-X-C motif chemokine receptor 6 [Gene - OMIM - HGNC]
CDCP1:CUB domain containing protein 1 [Gene - OMIM - HGNC]
CAMKV:CaM kinase like vesicle associated [Gene - OMIM - HGNC]
DALRD3:DALR anticodon binding domain containing 3 [Gene - OMIM - HGNC]
DCAF1:DDB1 and CUL4 associated factor 1 [Gene - OMIM - HGNC]
DHX30:DExH-box helicase 30 [Gene - OMIM - HGNC]
FBXW12:F-box and WD repeat domain containing 12 [Gene - OMIM - HGNC]
FYCO1:FYVE and coiled-coil domain autophagy adaptor 1 [Gene - OMIM - HGNC]
GNL3:G protein nucleolar 3 [Gene - OMIM - HGNC]
GNAI2:G protein subunit alpha i2 [Gene - OMIM - HGNC]
GNAT1:G protein subunit alpha transducin 1 [Gene - OMIM - HGNC]
GPR62:G protein-coupled receptor 62 [Gene - OMIM - HGNC]
GMPPB:GDP-mannose pyrophosphorylase B [Gene - OMIM - HGNC]
HEMK1:HemK methyltransferase family member 1 [Gene - OMIM - HGNC]
IQCF1:IQ motif containing F1 [Gene - HGNC]
IQCF2:IQ motif containing F2 [Gene - HGNC]
IQCF3:IQ motif containing F3 [Gene - HGNC]
IQCF5:IQ motif containing F5 [Gene - HGNC]
IQCF6:IQ motif containing F6 [Gene - HGNC]
LIMD1:LIM domain containing 1 [Gene - OMIM - HGNC]
MAPKAPK3:MAPK activated protein kinase 3 [Gene - OMIM - HGNC]
MON1A:MON1 homolog A, secretory trafficking associated [Gene - OMIM - HGNC]
NAA80:N-alpha-acetyltransferase 80, NatH catalytic subunit [Gene - OMIM - HGNC]
NDUFAF3:NADH:ubiquinone oxidoreductase complex assembly factor 3 [Gene - OMIM - HGNC]
NCKIPSD:NCK interacting protein with SH3 domain [Gene - OMIM - HGNC]
NEK4:NIMA related kinase 4 [Gene - OMIM - HGNC]
NME6:NME/NM23 nucleoside diphosphate kinase 6 [Gene - OMIM - HGNC]
NPRL2:NPR2 like, GATOR1 complex subunit [Gene - OMIM - HGNC]
PHF7:PHD finger protein 7 [Gene - OMIM - HGNC]
POC1A:POC1 centriolar protein A [Gene - OMIM - HGNC]
RAD54L2:RAD54 like 2 [Gene - OMIM - HGNC]
RFT1:RFT1 homolog [Gene - OMIM - HGNC]
RBM15B:RNA binding motif protein 15B [Gene - OMIM - HGNC]
RBM5:RNA binding motif protein 5 [Gene - OMIM - HGNC]
RBM6:RNA binding motif protein 6 [Gene - OMIM - HGNC]
RASSF1:Ras association domain family member 1 [Gene - OMIM - HGNC]
SACM1L:SAC1 like phosphatidylinositide phosphatase [Gene - OMIM - HGNC]
SEMA3F-AS1:SEMA3F antisense RNA 1 [Gene - HGNC]
SETD2:SET domain containing 2, histone lysine methyltransferase [Gene - OMIM - HGNC]
SCAP:SREBF chaperone [Gene - OMIM - HGNC]
STIMATE:STIM activating enhancer [Gene - OMIM - HGNC]
STIMATE-MUSTN1:STIMATE-MUSTN1 readthrough [Gene - HGNC]
SMARCC1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 [Gene - OMIM - HGNC]
SFMBT1:Scm like with four mbt domains 1 [Gene - OMIM - HGNC]
TCTA:T cell leukemia translocation altered [Gene - OMIM - HGNC]
TRAIP:TRAF interacting protein [Gene - OMIM - HGNC]
WDR6:WD repeat domain 6 [Gene - OMIM - HGNC]
WDR82:WD repeat domain 82 [Gene - OMIM - HGNC]
XCR1:X-C motif chemokine receptor 1 [Gene - OMIM - HGNC]
ABHD14A:abhydrolase domain containing 14A [Gene - OMIM - HGNC]
ABHD14B:abhydrolase domain containing 14B [Gene - HGNC]
APEH:acylaminoacyl-peptide hydrolase [Gene - OMIM - HGNC]
AMIGO3:adhesion molecule with Ig like domain 3 [Gene - OMIM - HGNC]
ACY1:aminoacylase 1 [Gene - OMIM - HGNC]
AMT:aminomethyltransferase [Gene - OMIM - HGNC]
ARIH2:ariadne RBR E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
BSN:bassoon presynaptic cytomatrix protein [Gene - OMIM - HGNC]
CELSR3:cadherin EGF LAG seven-pass G-type receptor 3 [Gene - OMIM - HGNC]
CDHR4:cadherin related family member 4 [Gene - HGNC]
CACNA2D2:calcium voltage-gated channel auxiliary subunit alpha2delta 2 [Gene - OMIM - HGNC]
CACNA1D:calcium voltage-gated channel subunit alpha1 D [Gene - OMIM - HGNC]
CAMP:cathelicidin antimicrobial peptide [Gene - OMIM - HGNC]
CDC25A:cell division cycle 25A [Gene - OMIM - HGNC]
CHDH:choline dehydrogenase [Gene - HGNC]
CSPG5:chondroitin sulfate proteoglycan 5 [Gene - OMIM - HGNC]
C3orf18:chromosome 3 open reading frame 18 [Gene - HGNC]
C3orf62:chromosome 3 open reading frame 62 [Gene - HGNC]
CIMIP7:ciliary microtubule inner protein 7 [Gene - HGNC]
CCDC12:coiled-coil domain containing 12 [Gene - HGNC]
CCDC51:coiled-coil domain containing 51 [Gene - OMIM - HGNC]
CCDC71:coiled-coil domain containing 71 [Gene - HGNC]
COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]
CRIPTO:cripto, EGF-CFC family member [Gene - OMIM - HGNC]
CYB561D2:cytochrome b561 family member D2 [Gene - OMIM - HGNC]
CISH:cytokine inducible SH2 containing protein [Gene - OMIM - HGNC]
DCP1A:decapping mRNA 1A [Gene - OMIM - HGNC]
DOCK3:dedicator of cytokinesis 3 [Gene - OMIM - HGNC]
DUSP7:dual specificity phosphatase 7 [Gene - OMIM - HGNC]
DNAH1:dynein axonemal heavy chain 1 [Gene - OMIM - HGNC]
DAG1:dystroglycan 1 [Gene - OMIM - HGNC]
ELP6:elongator acetyltransferase complex subunit 6 [Gene - OMIM - HGNC]
GRM2:glutamate metabotropic receptor 2 [Gene - OMIM - HGNC]
QRICH1:glutamine rich 1 [Gene - OMIM - HGNC]
QARS1:glutaminyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
GPX1:glutathione peroxidase 1 [Gene - OMIM - HGNC]
GLYCTK:glycerate kinase [Gene - OMIM - HGNC]
GLT8D1:glycosyltransferase 8 domain containing 1 [Gene - OMIM - HGNC]
HYAL1:hyaluronidase 1 [Gene - OMIM - HGNC]
HYAL2:hyaluronidase 2 [Gene - OMIM - HGNC]
HYAL3:hyaluronidase 3 [Gene - OMIM - HGNC]
INKA1:inka box actin regulator 1 [Gene - OMIM - HGNC]
IMPDH2:inosine monophosphate dehydrogenase 2 [Gene - OMIM - HGNC]
IP6K1:inositol hexakisphosphate kinase 1 [Gene - OMIM - HGNC]
IP6K2:inositol hexakisphosphate kinase 2 [Gene - OMIM - HGNC]
ITIH1:inter-alpha-trypsin inhibitor heavy chain 1 [Gene - OMIM - HGNC]
ITIH3:inter-alpha-trypsin inhibitor heavy chain 3 [Gene - OMIM - HGNC]
ITIH4:inter-alpha-trypsin inhibitor heavy chain 4 [Gene - OMIM - HGNC]
IHO1:interactor of HORMAD1 1 [Gene - OMIM - HGNC]
IFRD2:interferon related developmental regulator 2 [Gene - OMIM - HGNC]
KLHDC8B:kelch domain containing 8B [Gene - OMIM - HGNC]
KLHL18:kelch like family member 18 [Gene - OMIM - HGNC]
KIF9:kinesin family member 9 [Gene - OMIM - HGNC]
LTF:lactotransferrin [Gene - OMIM - HGNC]
LAMB2:laminin subunit beta 2 [Gene - OMIM - HGNC]
LRRC2:leucine rich repeat containing 2 [Gene - OMIM - HGNC]
LSMEM2:leucine rich single-pass membrane protein 2 [Gene - HGNC]
LZTFL1:leucine zipper transcription factor like 1 [Gene - OMIM - HGNC]
LARS2:leucyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
MST1R:macrophage stimulating 1 receptor [Gene - OMIM - HGNC]
MST1:macrophage stimulating 1 [Gene - OMIM - HGNC]
MANF:mesencephalic astrocyte derived neurotrophic factor [Gene - OMIM - HGNC]
MIR191:microRNA 191 [Gene - OMIM - HGNC]
MIRLET7G:microRNA let-7g [Gene - OMIM - HGNC]
MAP4:microtubule associated protein 4 [Gene - OMIM - HGNC]
MUSTN1:musculoskeletal, embryonic nuclear protein 1 [Gene - OMIM - HGNC]
MYL3:myosin light chain 3 [Gene - OMIM - HGNC]
NBEAL2:neurobeachin like 2 [Gene - OMIM - HGNC]
NICN1:nicolin 1, tubulin polyglutamylase complex subunit [Gene - OMIM - HGNC]
NISCH:nischarin [Gene - OMIM - HGNC]
PTH1R:parathyroid hormone 1 receptor [Gene - OMIM - HGNC]
PLXNB1:plexin B1 [Gene - OMIM - HGNC]
PARP3:poly(ADP-ribose) polymerase family member 3 [Gene - OMIM - HGNC]
PCBP4:poly(rC) binding protein 4 [Gene - OMIM - HGNC]
PBRM1:polybromo 1 [Gene - OMIM - HGNC]
P4HTM:prolyl 4-hydroxylase, transmembrane [Gene - OMIM - HGNC]
PRKCD:protein kinase C delta [Gene - OMIM - HGNC]
PRKAR2A:protein kinase cAMP-dependent type II regulatory subunit alpha [Gene - OMIM - HGNC]
PPM1M:protein phosphatase, Mg2+/Mn2+ dependent 1M [Gene - OMIM - HGNC]
PTPN23:protein tyrosine phosphatase non-receptor type 23 [Gene - OMIM - HGNC]
RHOA:ras homolog family member A [Gene - OMIM - HGNC]
RTP3:receptor transporter protein 3 [Gene - OMIM - HGNC]
RRP9:ribosomal RNA processing 9, U3 small nucleolar RNA binding protein [Gene - OMIM - HGNC]
RPL29:ribosomal protein L29 [Gene - OMIM - HGNC]
RNF123:ring finger protein 123 [Gene - OMIM - HGNC]
SEMA3B:semaphorin 3B [Gene - OMIM - HGNC]
SEMA3F:semaphorin 3F [Gene - OMIM - HGNC]
SEMA3G:semaphorin 3G [Gene - HGNC]
SPINK8:serine peptidase inhibitor Kazal type 8 (putative) [Gene - HGNC]
PRSS50:serine protease 50 [Gene - OMIM - HGNC]
SHISA5:shisa family member 5 [Gene - OMIM - HGNC]
SPCS1:signal peptidase complex subunit 1 [Gene - OMIM - HGNC]
SLC25A20:solute carrier family 25 member 20 [Gene - OMIM - HGNC]
SLC26A6:solute carrier family 26 member 6 [Gene - OMIM - HGNC]
SLC38A3:solute carrier family 38 member 3 [Gene - OMIM - HGNC]
SLC6A20:solute carrier family 6 member 20 [Gene - OMIM - HGNC]
STAB1:stabilin 1 [Gene - OMIM - HGNC]
TEX264:testis expressed 264, ER-phagy receptor [Gene - OMIM - HGNC]
TREX1:three prime repair exonuclease 1 [Gene - OMIM - HGNC]
TLR9:toll like receptor 9 [Gene - OMIM - HGNC]
TKT:transketolase [Gene - OMIM - HGNC]
TMA7:translation machinery associated 7 homolog [Gene - OMIM - HGNC]
TMIE:transmembrane inner ear [Gene - OMIM - HGNC]
TMEM115:transmembrane protein 115 [Gene - OMIM - HGNC]
TMEM158:transmembrane protein 158 [Gene - OMIM - HGNC]
TMEM89:transmembrane protein 89 [Gene - HGNC]
TNNC1:troponin C1, slow skeletal and cardiac type [Gene - OMIM - HGNC]
TUSC2:tumor suppressor 2, mitochondrial calcium regulator [Gene - OMIM - HGNC]
TWF2:twinfilin actin binding protein 2 [Gene - OMIM - HGNC]
UQCC5:ubiquinol-cytochrome c reductase complex assembly factor 5 [Gene - OMIM - HGNC]
UQCRC1:ubiquinol-cytochrome c reductase core protein 1 [Gene - OMIM - HGNC]
UBA7:ubiquitin like modifier activating enzyme 7 [Gene - OMIM - HGNC]
USP19:ubiquitin specific peptidase 19 [Gene - OMIM - HGNC]
USP4:ubiquitin specific peptidase 4 [Gene - OMIM - HGNC]
UCN2:urocortin 2 [Gene - OMIM - HGNC]
ZMYND10:zinc finger MYND-type containing 10 [Gene - OMIM - HGNC]
ZNF589:zinc finger protein 589 [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

3p21.31-21.1

Genomic location:

Chr3: 45153770 - 53878616 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616)

Observations:

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
SCV000898326	Baylor Genetics	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Pathogenic (Nov 1, 2018)	germline	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

SCV000898326

Baylor Genetics

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Pathogenic
(Nov 1, 2018)

germline

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	germline	yes	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee.

Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a.

PubMed [citation]

PMID:: 21681106

Details of each submission

From Baylor Genetics, SCV000898326.1

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

Description

Duplications involving this region have been previously reported in patients with low birth weight, short stature, microcephaly, and dysmorphic features [PMID 7246613]

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

Last Updated: Sep 1, 2024

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Relating variation to medicine