GRCh37/hg19 13q21.2-34(chr13:61534068-115107733)x3 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 28, 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:: RCV003484899.1

Allele description [Variation Report for GRCh37/hg19 13q21.2-34(chr13:61534068-115107733)x3]

GRCh37/hg19 13q21.2-34(chr13:61534068-115107733)x3

Genes:

ADPRHL1:ADP-ribosylhydrolase like 1 [Gene - OMIM - HGNC]
ANKRD10-IT1:ANKRD10 intronic transcript 1 [Gene - HGNC]
ABCC4:ATP binding cassette subfamily C member 4 (PEL blood group) [Gene - OMIM - HGNC]
ATP11AUN:ATP11A upstream neighbor lncRNA [Gene - HGNC]
ATP4B:ATPase H+/K+ transporting subunit beta [Gene - OMIM - HGNC]
ATP11A:ATPase phospholipid transporting 11A [Gene - OMIM - HGNC]
ATXN8OS:ATXN8 opposite strand lncRNA [Gene - OMIM - HGNC]
BIVM-ERCC5:BIVM-ERCC5 readthrough [Gene - HGNC]
BORA:BORA aurora kinase A activator [Gene - OMIM - HGNC]
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
COMMD6:COMM domain containing 6 [Gene - OMIM - HGNC]
DAOA:D-amino acid oxidase activator [Gene - OMIM - HGNC]
DAOA-AS1:DAOA antisense RNA 1 [Gene - OMIM - HGNC]
DZIP1:DAZ interacting zinc finger protein 1 [Gene - OMIM - HGNC]
DIS3:DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease [Gene - OMIM - HGNC]
LIG4:DNA ligase 4 [Gene - OMIM - HGNC]
DNAJC3:DnaJ heat shock protein family (Hsp40) member C3 [Gene - OMIM - HGNC]
ERCC5:ERCC excision repair 5, endonuclease [Gene - OMIM - HGNC]
FBXL3:F-box and leucine rich repeat protein 3 [Gene - OMIM - HGNC]
FARP1:FERM, ARH/RhoGEF and pleckstrin domain protein 1 [Gene - OMIM - HGNC]
GPR180:G protein-coupled receptor 180 [Gene - OMIM - HGNC]
GPR183:G protein-coupled receptor 183 [Gene - OMIM - HGNC]
GPR18:G protein-coupled receptor 18 [Gene - OMIM - HGNC]
KLF12:KLF transcription factor 12 [Gene - OMIM - HGNC]
KLF5:KLF transcription factor 5 [Gene - OMIM - HGNC]
LMO7:LIM domain 7 [Gene - OMIM - HGNC]
LMO7DN:LMO7 downstream neighbor [Gene - HGNC]
MCF2L:MCF.2 cell line derived transforming sequence like [Gene - OMIM - HGNC]
MIR4500HG:MIR4500 host gene [Gene - HGNC]
MYCBP2:MYC binding protein 2 [Gene - OMIM - HGNC]
NAXD:NAD(P)HX dehydratase [Gene - OMIM - HGNC]
NALF1:NALCN channel auxiliary factor 1 [Gene - OMIM - HGNC]
NDFIP2:Nedd4 family interacting protein 2 [Gene - OMIM - HGNC]
OBI1:ORC ubiquitin ligase 1 [Gene - OMIM - HGNC]
PCID2:PCI domain containing 2 [Gene - OMIM - HGNC]
POU4F1:POU class 4 homeobox 1 [Gene - OMIM - HGNC]
RAB20:RAB20, member RAS oncogene family [Gene - HGNC]
RAP2A:RAP2A, member of RAS oncogene family [Gene - OMIM - HGNC]
RASA3:RAS p21 protein activator 3 [Gene - OMIM - HGNC]
RBM26:RNA binding motif protein 26 [Gene - OMIM - HGNC]
ARHGEF7:Rho guanine nucleotide exchange factor 7 [Gene - OMIM - HGNC]
SLAIN1:SLAIN motif family member 1 [Gene - OMIM - HGNC]
SLITRK1:SLIT and NTRK like family member 1 [Gene - OMIM - HGNC]
SLITRK5:SLIT and NTRK like family member 5 [Gene - OMIM - HGNC]
SLITRK6:SLIT and NTRK like family member 6 [Gene - OMIM - HGNC]
SOX1:SRY-box transcription factor 1 [Gene - OMIM - HGNC]
SOX21:SRY-box transcription factor 21 [Gene - OMIM - HGNC]
SWINGN:SWI/SNF complex interacting GAS6 enhancer non-coding RNA [Gene - HGNC]
TBC1D4:TBC1 domain family member 4 [Gene - OMIM - HGNC]
TGDS:TDP-glucose 4,6-dehydratase [Gene - OMIM - HGNC]
TNFSF13B:TNF superfamily member 13b [Gene - OMIM - HGNC]
UBAC2:UBA domain containing 2 [Gene - HGNC]
UGGT2:UDP-glucose glycoprotein glucosyltransferase 2 [Gene - OMIM - HGNC]
UPF3A:UPF3A regulator of nonsense mediated mRNA decay [Gene - OMIM - HGNC]
ZIC2:Zic family member 2 [Gene - OMIM - HGNC]
ZIC5:Zic family member 5 [Gene - OMIM - HGNC]
ABHD13:abhydrolase domain containing 13 [Gene - HGNC]
ACOD1:aconitate decarboxylase 1 [Gene - OMIM - HGNC]
ANKRD10:ankyrin repeat domain 10 [Gene - HGNC]
ARGLU1:arginine and glutamate rich 1 [Gene - OMIM - HGNC]
BIVM:basic, immunoglobulin-like variable motif containing [Gene - OMIM - HGNC]
CDC16:cell division cycle 16 [Gene - OMIM - HGNC]
CHAMP1:chromosome alignment maintaining phosphoprotein 1 [Gene - OMIM - HGNC]
CLYBL:citramalyl-CoA lyase [Gene - OMIM - HGNC]
CLDN10:claudin 10 [Gene - OMIM - HGNC]
F7:coagulation factor VII [Gene - OMIM - HGNC]
F10:coagulation factor X [Gene - OMIM - HGNC]
CCDC168:coiled-coil domain containing 168 [Gene - HGNC]
COL4A1:collagen type IV alpha 1 chain [Gene - OMIM - HGNC]
COL4A2:collagen type IV alpha 2 chain [Gene - OMIM - HGNC]
CUL4A:cullin 4A [Gene - OMIM - HGNC]
CARS2:cysteinyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
DACH1:dachshund family transcription factor 1 [Gene - OMIM - HGNC]
DOCK9:dedicator of cytokinesis 9 [Gene - OMIM - HGNC]
DCUN1D2:defective in cullin neddylation 1 domain containing 2 [Gene - HGNC]
DCT:dopachrome tautomerase [Gene - OMIM - HGNC]
EDNRB:endothelin receptor type B [Gene - OMIM - HGNC]
EFNB2:ephrin B2 [Gene - OMIM - HGNC]
FGF14:fibroblast growth factor 14 [Gene - OMIM - HGNC]
GGACT:gamma-glutamylamine cyclotransferase [Gene - OMIM - HGNC]
GPC5:glypican 5 [Gene - OMIM - HGNC]
GPC6:glypican 6 [Gene - OMIM - HGNC]
GAS6:growth arrest specific 6 [Gene - OMIM - HGNC]
GRTP1:growth hormone regulated TBC protein 1 [Gene - OMIM - HGNC]
HS6ST3:heparan sulfate 6-O-sulfotransferase 3 [Gene - OMIM - HGNC]
IPO5:importin 5 [Gene - OMIM - HGNC]
ING1:inhibitor of growth family member 1 [Gene - OMIM - HGNC]
IRS2:insulin receptor substrate 2 [Gene - OMIM - HGNC]
ITGBL1:integrin subunit beta like 1 [Gene - OMIM - HGNC]
KLHL1:kelch like family member 1 [Gene - OMIM - HGNC]
LINC00402:long intergenic non-protein coding RNA 402 [Gene - HGNC]
LINC00567:long intergenic non-protein coding RNA 567 [Gene - HGNC]
LAMP1:lysosomal associated membrane protein 1 [Gene - OMIM - HGNC]
METTL21C:methyltransferase 21C, AARS1 lysine [Gene - OMIM - HGNC]
MIR17HG:miR-17-92a-1 cluster host gene [Gene - OMIM - HGNC]
MIR17:microRNA 17 [Gene - OMIM - HGNC]
MIR18A:microRNA 18a [Gene - OMIM - HGNC]
MIR19A:microRNA 19a [Gene - OMIM - HGNC]
MIR19B1:microRNA 19b-1 [Gene - OMIM - HGNC]
MIR20A:microRNA 20a [Gene - OMIM - HGNC]
MIR92A1:microRNA 92a-1 [Gene - OMIM - HGNC]
MZT1:mitotic spindle organizing protein 1 [Gene - OMIM - HGNC]
MBNL2:muscleblind like splicing regulator 2 [Gene - OMIM - HGNC]
MYO16:myosin XVI [Gene - OMIM - HGNC]
OXGR1:oxoglutarate receptor 1 [Gene - OMIM - HGNC]
KCTD12:potassium channel tetramerization domain containing 12 [Gene - OMIM - HGNC]
PIBF1:progesterone immunomodulatory binding factor 1 [Gene - OMIM - HGNC]
PCCA:propionyl-CoA carboxylase subunit alpha [Gene - OMIM - HGNC]
POGLUT2:protein O-glucosyltransferase 2 [Gene - OMIM - HGNC]
PROZ:protein Z, vitamin K dependent plasma glycoprotein [Gene - OMIM - HGNC]
PCDH20:protocadherin 20 [Gene - OMIM - HGNC]
PCDH9:protocadherin 9 [Gene - OMIM - HGNC]
RNF113B:ring finger protein 113B [Gene - HGNC]
SCEL:sciellin [Gene - OMIM - HGNC]
STK24:serine/threonine kinase 24 [Gene - OMIM - HGNC]
NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]
SLC10A2:solute carrier family 10 member 2 [Gene - OMIM - HGNC]
SLC15A1:solute carrier family 15 member 1 [Gene - OMIM - HGNC]
SPACA7:sperm acrosome associated 7 [Gene - HGNC]
SPRY2:sprouty RTK signaling antagonist 2 [Gene - OMIM - HGNC]
TEX29:testis expressed 29 [Gene - HGNC]
TEX30:testis expressed 30 [Gene - HGNC]
TFDP1:transcription factor Dp-1 [Gene - OMIM - HGNC]
TM9SF2:transmembrane 9 superfamily member 2 [Gene - OMIM - HGNC]
TMTC4:transmembrane O-mannosyltransferase targeting cadherins 4 [Gene - OMIM - HGNC]
TMCO3:transmembrane and coiled-coil domains 3 [Gene - OMIM - HGNC]
TMEM255B:transmembrane protein 255B [Gene - HGNC]
TPP2:tripeptidyl peptidase 2 [Gene - OMIM - HGNC]
TUBGCP3:tubulin gamma complex component 3 [Gene - OMIM - HGNC]
UCHL3:ubiquitin C-terminal hydrolase L3 [Gene - OMIM - HGNC]
LOC100288208:uncharacterized LOC100288208 [Gene]

Variant type:

copy number gain

Cytogenetic location:

13q21.2-34

Genomic location:

Chr13: 61534068 - 115107733 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 13q21.2-34(chr13:61534068-115107733)x3

HGVS:

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
SCV004230760	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Jan 28, 2023)	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

SCV004230760

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Jan 28, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004230760.1

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

Description

Duplications of the 13q terminal region are associated with a range of phenotypic outcomes (Brogna 2020, Douglas 2017, Habedank 1979, Krygier 2014, Phadke 2004, Ribacoba 2008, Rivas 1984, Tharapel 1984, Wei 2012). Therefore, based on current medical literature, this copy number variant (CNV) is classified as pathogenic. References: Brogna et al., Brain Sci. 2020 Dec 26;11(1):21. PMID: 33375380 Douglas et al., Am J Med Genet A. 2017 Jun;173(6):1673-1680. PMID: 28394407 Habedank et al., Hum Genet. 1979 Nov 1;52(1):91-9. PMID: 527979 Krygier et al., Clin Dysmorphol. 2014 Oct;23(4):155-7. PMID: 25144153 Phadke et al., Indian Pediatr. 2004 Jun;41(6):614-7. PMID: 15235171 Ribacoba et al., Int Arch Med. 2008 Apr 29;1(1):5. PMID: 18471271 Rivas et al., Hum Genet. 1984;67(1):86-93. PMID: 6745930 Tharapel et al., Indian J Pediatr. 1984 Jul-Aug;51(411):481-7. PMID: 6526455 Wei et al., Case Rep Genet. 2012;2012:821347. PMID: 23133763

#	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: Sep 1, 2024

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