GRCh37/hg19 13q22.1-34(chr13:73488238-115107733)x3 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 4, 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:: RCV003484901.1

Allele description [Variation Report for GRCh37/hg19 13q22.1-34(chr13:73488238-115107733)x3]

GRCh37/hg19 13q22.1-34(chr13:73488238-115107733)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]
BIVM-ERCC5:BIVM-ERCC5 readthrough [Gene - 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]
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]
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 - 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]
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]
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]
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:

13q22.1-34

Genomic location:

Chr13: 73488238 - 115107733 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 13q22.1-34(chr13:73488238-115107733)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
SCV004230762	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Jan 4, 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

SCV004230762

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Jan 4, 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, SCV004230762.1

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

Description

Patients with partial trisomy of the distal segment of chromosome 13q (13q14qter) have been described to have a similar phenotype as patients with complete trisomy 13. Phenotypic features include facial clefting, seizures, deafness, and heart defects (Warburton et al., Am J Hum Genet 2000 Jun;66(6):1794-806.PMID: 10777715). Milder phenotypes have been observed in patients with 13q partial trisomy (q14-qter) (Krygier et al., Clin Dysmorphol. 2014 Oct;23(4):155-7. PMID: 25144153). Thus, based on current medical literature and gene content this copy number gain 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: Feb 4, 2024

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Relating variation to medicine