GRCh37/hg19 8p23.3-22(chr8:158049-18936715)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 26, 2021
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:: RCV002472557.1

Allele description [Variation Report for GRCh37/hg19 8p23.3-22(chr8:158049-18936715)x1]

GRCh37/hg19 8p23.3-22(chr8:158049-18936715)x1

Genes:

AGPAT5:1-acylglycerol-3-phosphate O-acyltransferase 5 [Gene - OMIM - HGNC]
ASAH1-AS1:ASAH1 antisense RNA 1 [Gene - HGNC]
BLK:BLK proto-oncogene, Src family tyrosine kinase [Gene - OMIM - HGNC]
CNOT7:CCR4-NOT transcription complex subunit 7 [Gene - OMIM - HGNC]
CLN8:CLN8 transmembrane ER and ERGIC protein [Gene - OMIM - HGNC]
CSMD1:CUB and Sushi multiple domains 1 [Gene - OMIM - HGNC]
DLC1:DLC1 Rho GTPase activating protein [Gene - OMIM - HGNC]
DLGAP2:DLG associated protein 2 [Gene - OMIM - HGNC]
FBXO25:F-box protein 25 [Gene - OMIM - HGNC]
GATA4:GATA binding protein 4 [Gene - OMIM - HGNC]
LONRF1:LON peptidase N-terminal domain and ring finger 1 [Gene - HGNC]
NAT1:N-acetyltransferase 1 [Gene - OMIM - HGNC]
NAT2:N-acetyltransferase 2 [Gene - OMIM - HGNC]
ASAH1:N-acylsphingosine amidohydrolase 1 [Gene - OMIM - HGNC]
PINX1:PIN2 (TERF1) interacting telomerase inhibitor 1 [Gene - OMIM - HGNC]
RP1L1:RP1 like 1 [Gene - OMIM - HGNC]
ARHGEF10:Rho guanine nucleotide exchange factor 10 [Gene - OMIM - HGNC]
SOX7:SRY-box transcription factor 7 [Gene - OMIM - HGNC]
VPS37A:VPS37A subunit of ESCRT-I [Gene - OMIM - HGNC]
XKR5:XK related 5 [Gene - HGNC]
XKR6:XK related 6 [Gene - HGNC]
ANGPT2:angiopoietin 2 [Gene - OMIM - HGNC]
CTSB:cathepsin B [Gene - OMIM - HGNC]
C8orf48:chromosome 8 open reading frame 48 [Gene - HGNC]
C8orf74:chromosome 8 open reading frame 74 [Gene - HGNC]
CLDN23:claudin 23 [Gene - OMIM - HGNC]
DEFA1:defensin alpha 1 [Gene - OMIM - HGNC]
DEFA1B:defensin alpha 1B [Gene - HGNC]
DEFA3:defensin alpha 3 [Gene - OMIM - HGNC]
DEFA4:defensin alpha 4 [Gene - OMIM - HGNC]
DEFA5:defensin alpha 5 [Gene - OMIM - HGNC]
DEFA6:defensin alpha 6 [Gene - OMIM - HGNC]
DEFB103A:defensin beta 103A [Gene - HGNC]
DEFB103B:defensin beta 103B [Gene - OMIM - HGNC]
DEFB104A:defensin beta 104A [Gene - HGNC]
DEFB104B:defensin beta 104B [Gene - HGNC]
DEFB105A:defensin beta 105A [Gene - HGNC]
DEFB105B:defensin beta 105B [Gene - HGNC]
DEFB106A:defensin beta 106A [Gene - HGNC]
DEFB106B:defensin beta 106B [Gene - HGNC]
DEFB107A:defensin beta 107A [Gene - HGNC]
DEFB107B:defensin beta 107B [Gene - HGNC]
DEFB130A:defensin beta 130A [Gene - HGNC]
DEFB134:defensin beta 134 [Gene - HGNC]
DEFB135:defensin beta 135 [Gene - HGNC]
DEFB136:defensin beta 136 [Gene - HGNC]
DEFB1:defensin beta 1 [Gene - OMIM - HGNC]
DEFB4A:defensin beta 4A [Gene - OMIM - HGNC]
DEFB4B:defensin beta 4B [Gene - HGNC]
ERI1:exoribonuclease 1 [Gene - OMIM - HGNC]
FAM167A:family with sequence similarity 167 member A [Gene - OMIM - HGNC]
FAM86B1:family with sequence similarity 86 member B1 [Gene - OMIM - HGNC]
FAM86B2:family with sequence similarity 86 member B2 [Gene - OMIM - HGNC]
FDFT1:farnesyl-diphosphate farnesyltransferase 1 [Gene - OMIM - HGNC]
FGL1:fibrinogen like 1 [Gene - OMIM - HGNC]
FGF20:fibroblast growth factor 20 [Gene - OMIM - HGNC]
ERICH1:glutamate rich 1 [Gene - HGNC]
KBTBD11:kelch repeat and BTB domain containing 11 [Gene - OMIM - HGNC]
MSR1:macrophage scavenger receptor 1 [Gene - OMIM - HGNC]
MSRA:methionine sulfoxide reductase A [Gene - OMIM - HGNC]
MIR124-1:microRNA 124-1 [Gene - OMIM - HGNC]
MCPH1:microcephalin 1 [Gene - OMIM - HGNC]
MTUS1:microtubule associated scaffold protein 1 [Gene - OMIM - HGNC]
MICU3:mitochondrial calcium uptake family member 3 [Gene - OMIM - HGNC]
MFHAS1:multifunctional ROCO family signaling regulator 1 [Gene - OMIM - HGNC]
MYOM2:myomesin 2 [Gene - OMIM - HGNC]
MTMR7:myotubularin related protein 7 [Gene - OMIM - HGNC]
MTMR9:myotubularin related protein 9 [Gene - OMIM - HGNC]
NEIL2:nei like DNA glycosylase 2 [Gene - OMIM - HGNC]
PCM1:pericentriolar material 1 [Gene - OMIM - HGNC]
PDGFRL:platelet derived growth factor receptor like [Gene - OMIM - HGNC]
PSD3:pleckstrin and Sec7 domain containing 3 [Gene - OMIM - HGNC]
PPP1R3B:protein phosphatase 1 regulatory subunit 3B [Gene - OMIM - HGNC]
SGCZ:sarcoglycan zeta [Gene - OMIM - HGNC]
PRSS51:serine protease 51 [Gene - HGNC]
PRSS55:serine protease 55 [Gene - OMIM - HGNC]
SLC35G5:solute carrier family 35 member G5 [Gene - OMIM - HGNC]
SLC7A2:solute carrier family 7 member 2 [Gene - OMIM - HGNC]
SPAG11A:sperm associated antigen 11A [Gene - HGNC]
SPAG11B:sperm associated antigen 11B [Gene - OMIM - HGNC]
TRMT9B:tRNA methyltransferase 9B (putative) [Gene - OMIM - HGNC]
TNKS:tankyrase [Gene - OMIM - HGNC]
TDRP:testis development related protein [Gene - OMIM - HGNC]
TUSC3:tumor suppressor candidate 3 [Gene - OMIM - HGNC]
USP17L1:ubiquitin specific peptidase 17 like family member 1 [Gene - HGNC]
USP17L2:ubiquitin specific peptidase 17 like family member 2 [Gene - OMIM - HGNC]
USP17L3:ubiquitin specific peptidase 17 like family member 3 [Gene - HGNC]
USP17L4:ubiquitin specific peptidase 17 like family member 4 [Gene - HGNC]
USP17L7:ubiquitin specific peptidase 17 like family member 7 [Gene - HGNC]
USP17L8:ubiquitin specific peptidase 17 like family member 8 [Gene - HGNC]
ZDHHC2:zinc finger DHHC-type palmitoyltransferase 2 [Gene - OMIM - HGNC]
ZNF596:zinc finger protein 596 [Gene - HGNC]
ZNF705B:zinc finger protein 705B [Gene - HGNC]
ZNF705D:zinc finger protein 705D [Gene - HGNC]
ZNF705G:zinc finger protein 705G [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

8p23.3-22

Genomic location:

Chr8: 158049 - 18936715 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 8p23.3-22(chr8:158049-18936715)x1

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002772425	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Aug 26, 2021)	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

SCV002772425

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Aug 26, 2021)

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.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002772425.1

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

Description

The copy number loss of 8p23.3p22 involves multiple protein coding genes, including CLN8 (OMIM 607837), ARHGEF10 (OMIM 608136), CSMD1 (OMIM 608397), DLGAP2 (OMIM 605438), and GATA4 (OMIM 600576), and is expected to cause phenotypic and/or developmental abnormalities. Patients with comparable or smaller deletions of this region have a variable phenotype, including developmental delay and/or intellectual disability, neurobehavioral disorders, and craniofacial abnormalities. Congenital anomalies, such as heart defects and diaphragmatic hernia, were also reported in some patients (Shi 2017; Burnside 2013; Chien 2010; Kumar 2018). In particular, Perez et al reported a 15 Mb deletion at this locus in a fetus with increased nuchal translucency and diaphragmatic hernia (Perez 2018). A 13.32 Mb deletion of this locus was also reported in a patient with pulmonary stenosis, aortic stenosis, large ventricular septal defect, mild arch hypoplasia, bicuspid aortic valve and intrauterine growth restriction (Lazier 2016). Shi et al proposed that DLGAP2, CLN8, ARHGEF10 and CSMD1 are candidate genes for the deletion phenotype, and haploinsufficiency of GATA4 is associated with multiple cardiac diseases including atrial septal defect 2 (OMIM 607941). This large deletion also includes a few genes that are associated with OMIM phenotypes: ANGPT2 (OMIM 619369), RP1L1 (OMIM 613587 and 618826), BLK (OMIM 613375), CTSB (OMIM 148370), MCPH1 (OMIM 251200), FDFT1 (OMIM 618156 ), ASAH1 (OMIM 228000 and 159950), TUSC3 (OMIM 611093), and VPS37A (OMIM 614898). Reference Burnside et al. Am J Med Genet A. 2013 Apr;161A(4):822-8. PMID: 23495222. Chien et al. Clin Genet. 2010 Nov;78(5):449-56. PMID: 20236125. Kumar et al., J Pediatr Genet. 2018 Sep;7(3):125-129. PMID: 30105121. Lazier et al., J Obstet Gynaecol Can. 2016 Jul;38(7):619-26. PMID: 27591345. Maccarini et al., Mol Cytogenet. 2020 Jun 22;13:23. PMID: 32582378. Perez et al., Gynecol Obstet (Sunnyvale) 2018, 8:7 DOI: 10.4172/2161-0932.1000479. Shi et al. Mol Med Rep. 2017 Nov;16(5):6837-6845. PMID: 28901431. Tannour-Louet et al., Nat Med. 2014 Jul;20(7):715-24. PMID: 24880616.

#	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: Mar 26, 2023

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