GRCh37/hg19 7q21.3(chr7:94813388-96264152)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 22, 2022
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:: RCV003482969.1

Allele description [Variation Report for GRCh37/hg19 7q21.3(chr7:94813388-96264152)x1]

GRCh37/hg19 7q21.3(chr7:94813388-96264152)x1

Genes:

ASB4:ankyrin repeat and SOCS box containing 4 [Gene - OMIM - HGNC]
C7orf76:chromosome 7 open reading frame 76 [Gene - HGNC]
DYNC1I1:dynein cytoplasmic 1 intermediate chain 1 [Gene - OMIM - HGNC]
PON1:paraoxonase 1 [Gene - OMIM - HGNC]
PON2:paraoxonase 2 [Gene - OMIM - HGNC]
PON3:paraoxonase 3 [Gene - OMIM - HGNC]
PPP1R9A:protein phosphatase 1 regulatory subunit 9A [Gene - OMIM - HGNC]
PDK4:pyruvate dehydrogenase kinase 4 [Gene - OMIM - HGNC]
SLC25A13:solute carrier family 25 member 13 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

7q21.3

Genomic location:

Chr7: 94813388 - 96264152 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 7q21.3(chr7:94813388-96264152)x1

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
SCV004231486	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Sep 22, 2022)	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

SCV004231486

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Sep 22, 2022)

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, SCV004231486.1

#	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 7q21.3 involves multiple protein-coding genes. Copy number losses within and overlapping the current interval have been reported in several individuals with split hand/foot malformation 1 (OMIM 183600, Kouwenhoven 2010, Rasmussen 2016). A deletion within the current interval segregated with affected individuals over multiple generations of paternal transmission (Rattanasopha 2014). Furthermore, hemizygous deletions of PPP1R9A have been identified in patients with developmental delay (Uddin 2016). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic. References: Kouwenhoven et al., PLoS Genet. 2010 Aug 19;6(8):e1001065. PMID: 20808887 Rasmussen et al., Hum Genet. 2016 Mar;135(3):345-57. PMID: 26839112 Rattanasopha et al., J Med Genet. 2014 Dec;51(12):817-23. PMID: 25332435 Uddin et al., Sci Rep. 2016 Jul 1;6:28663. PMID: 27363808

#	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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