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

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005062995Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 22, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 7, 2024