NC_000005.9:g.(?_171765373)_(172662086_?)del AND Atrial septal defect 7

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 22, 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:: RCV004579004.1

Allele description

NC_000005.9:g.(?_171765373)_(172662086_?)del

Genes:

ATP6V0E1:ATPase H+ transporting V0 subunit e1 [Gene - OMIM - HGNC]
BNIP1:BCL2 interacting protein 1 [Gene - OMIM - HGNC]
CREBRF:CREB3 regulatory factor [Gene - OMIM - HGNC]
NKX2-5:NK2 homeobox 5 [Gene - OMIM - HGNC]
SH3PXD2B:SH3 and PX domains 2B [Gene - OMIM - HGNC]
DUSP1:dual specificity phosphatase 1 [Gene - OMIM - HGNC]
ERGIC1:endoplasmic reticulum-golgi intermediate compartment 1 [Gene - OMIM - HGNC]
NEURL1B:neuralized E3 ubiquitin protein ligase 1B [Gene - OMIM - HGNC]
RPL26L1:ribosomal protein L26 like 1 [Gene - HGNC]
SNORA74B:small nucleolar RNA, H/ACA box 74B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q35.1

Genomic location:

Chr5: 171765373 - 172662086 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_171765373)_(172662086_?)del

HGVS:

NC_000005.9:g.(?_171765373)_(172662086_?)del

Condition(s)

Name:: Atrial septal defect 7
Synonyms:: Atrial septal defect with atrioventricular conduction defects; ASD WITH OR WITHOUT ATRIOVENTRICULAR CONDUCTION DEFECTS; Atrial septal defect 7 with or without atrioventricular conduction defects; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007173; MedGen: C3276096; Orphanet: 1479; OMIM: 108900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005062995	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 22, 2023)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17891520, 20456451, 25205790, 26014430, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005062995

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 22, 2023)

unknown

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

A novel stop mutation truncating critical regions of the cardiac transcription factor NKX2-5 in a large family with autosomal-dominant inherited congenital heart disease.

Pabst S, Wollnik B, Rohmann E, Hintz Y, Glänzer K, Vetter H, Nickenig G, Grohé C.

Clin Res Cardiol. 2008 Jan;97(1):39-42. Epub 2007 Sep 25.

PubMed [citation]

PMID:: 17891520

Mutational spectrum in the cardiac transcription factor gene NKX2.5 (CSX) associated with congenital heart disease.

Stallmeyer B, Fenge H, Nowak-Göttl U, Schulze-Bahr E.

Clin Genet. 2010 Dec;78(6):533-40. doi: 10.1111/j.1399-0004.2010.01422.x.

PubMed [citation]

PMID:: 20456451

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV005062995.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the NKX2-5 gene has been identified. Loss-of-function variants in NKX2-5 are known to be pathogenic (PMID: 17891520, 20456451). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with atrial septal defect and atrioventricular block (PMID: 25205790, 26014430). For these reasons, this variant has been 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: Jul 7, 2024

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