GRCh37/hg19 7p14.1-12.3(chr7:42516660-46202495)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 5, 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:: RCV003482956.1

Allele description [Variation Report for GRCh37/hg19 7p14.1-12.3(chr7:42516660-46202495)x1]

GRCh37/hg19 7p14.1-12.3(chr7:42516660-46202495)x1

Genes:

AEBP1:AE binding protein 1 [Gene - OMIM - HGNC]
CCM2:CCM2 scaffold protein [Gene - OMIM - HGNC]
DDX56:DEAD-box helicase 56 [Gene - OMIM - HGNC]
POLD2:DNA polymerase delta 2, accessory subunit [Gene - OMIM - HGNC]
POLM:DNA polymerase mu [Gene - OMIM - HGNC]
H2AZ2:H2A.Z variant histone 2 [Gene - OMIM - HGNC]
HECW1:HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]
HECW1-IT1:HECW1 intronic transcript 1 [Gene - HGNC]
NACAD:NAC alpha domain containing [Gene - OMIM - HGNC]
NPC1L1:NPC1 like intracellular cholesterol transporter 1 [Gene - OMIM - HGNC]
NUDCD3:NudC domain containing 3 [Gene - OMIM - HGNC]
YKT6:YKT6 v-SNARE homolog [Gene - OMIM - HGNC]
ADCY1:adenylate cyclase 1 [Gene - OMIM - HGNC]
BLVRA:biliverdin reductase A [Gene - OMIM - HGNC]
CAMK2B:calcium/calmodulin dependent protein kinase II beta [Gene - OMIM - HGNC]
C7orf25:chromosome 7 open reading frame 25 [Gene - HGNC]
COA1:cytochrome c oxidase assembly factor 1 [Gene - OMIM - HGNC]
DBNL:drebrin like [Gene - OMIM - HGNC]
GCK:glucokinase [Gene - OMIM - HGNC]
IGFBP1:insulin like growth factor binding protein 1 [Gene - OMIM - HGNC]
IGFBP3:insulin like growth factor binding protein 3 [Gene - OMIM - HGNC]
MRPL32:mitochondrial ribosomal protein L32 [Gene - OMIM - HGNC]
MRPS24:mitochondrial ribosomal protein S24 [Gene - OMIM - HGNC]
MYO1G:myosin IG [Gene - OMIM - HGNC]
MYL7:myosin light chain 7 [Gene - OMIM - HGNC]
OGDH:oxoglutarate dehydrogenase [Gene - OMIM - HGNC]
PPIA:peptidylprolyl isomerase A [Gene - OMIM - HGNC]
PGAM2:phosphoglycerate mutase 2 [Gene - OMIM - HGNC]
PSMA2:proteasome 20S subunit alpha 2 [Gene - OMIM - HGNC]
PURB:purine rich element binding protein B [Gene - OMIM - HGNC]
RAMP3:receptor activity modifying protein 3 [Gene - OMIM - HGNC]
STK17A:serine/threonine kinase 17a [Gene - OMIM - HGNC]
SNHG15:small nucleolar RNA host gene 15 [Gene - HGNC]
SNORA5C:small nucleolar RNA, H/ACA box 5C [Gene - OMIM - HGNC]
SPDYE1:speedy/RINGO cell cycle regulator family member E1 [Gene - OMIM - HGNC]
TBRG4:transforming growth factor beta regulator 4 [Gene - OMIM - HGNC]
TMED4:transmembrane p24 trafficking protein 4 [Gene - OMIM - HGNC]
UBE2D4:ubiquitin conjugating enzyme E2 D4 (putative) [Gene - HGNC]
URGCP:upregulator of cell proliferation [Gene - OMIM - HGNC]
ZMIZ2:zinc finger MIZ-type containing 2 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

7p14.1-12.3

Genomic location:

Chr7: 42516660 - 46202495 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 7p14.1-12.3(chr7:42516660-46202495)x1

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Metagenome-assembled genome: SRR11784293_bin.17_metaWRAP_v1.3_MAG
Metagenome-assembled genome: SRR11784293_bin.17_metaWRAP_v1.3_MAG

biosample
cytochrome c oxidase subunit I (mitochondrion) [Canis lupus familiaris]
cytochrome c oxidase subunit I (mitochondrion) [Canis lupus familiaris]
gi|2733868501|gb|XAW20634.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004231473	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (May 5, 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

SCV004231473

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(May 5, 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, SCV004231473.1

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

Description

This loss involves multiple protein-coding genes associated with autosomal dominant disorders. Germline haploinsufficiency of CCM2 is associated with autosomal dominant cerebral cavernous malformations-2, with incomplete penetrance (D'Angelo 2011, Felbor 2007, Liquori 2007, Liquori 2008, Nardella 2018, Rath 2016, Riant 2013). Additionally, heterozygous missense and loss-of-function variants of GCK have been reported in association with multiple autosomal dominant forms of diabetes (OMIM 125851, 125853, 602485). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Therefore, based on size, gene content, and current medical literature, this copy number variant (CNV) is classified as pathogenic. References: D'Angelo et al., Brain Pathol. 2011 Mar;21(2):215-24. PMID: 21029238 Felbor et al., Neurogenetics. 2007 Apr;8(2):149-53. PMID: 17211633 Liquori et al., Am J Hum Genet. 2007 Jan;80(1):69-75. PMID: 17160895 Liquori et al., Neurogenetics. 2008 Feb;9(1):25-31. PMID: 18060436 Nardella et al., Hum Mutat. 2018 Dec;39(12):1885-1900. PMID: 30161288 Rath et al., Mol Genet Genomic Med. 2016 Dec 20;5(1):21-27. PMID: 28116327 Riant et al., Neurogenetics. 2013 May;14(2):133-41. PMID: 23595507

#	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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