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NM_004387.4(NKX2-5):c.65A>C (p.Gln22Pro) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 18, 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:
RCV000786392.2

Allele description [Variation Report for NM_004387.4(NKX2-5):c.65A>C (p.Gln22Pro)]

NM_004387.4(NKX2-5):c.65A>C (p.Gln22Pro)

Gene:
NKX2-5:NK2 homeobox 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q35.1
Genomic location:
Preferred name:
NM_004387.4(NKX2-5):c.65A>C (p.Gln22Pro)
HGVS:
  • NC_000005.10:g.173235019T>G
  • NG_013340.1:g.5294A>C
  • NM_001166175.2:c.65A>C
  • NM_001166176.2:c.65A>C
  • NM_004387.4:c.65A>CMANE SELECT
  • NP_001159647.1:p.Gln22Pro
  • NP_001159648.1:p.Gln22Pro
  • NP_004378.1:p.Gln22Pro
  • LRG_671t1:c.65A>C
  • LRG_671:g.5294A>C
  • LRG_671p1:p.Gln22Pro
  • NC_000005.9:g.172662022T>G
  • NM_004387.3:c.65A>C
Protein change:
Q22P
Links:
dbSNP: rs201442000
NCBI 1000 Genomes Browser:
rs201442000
Molecular consequence:
  • NM_001166175.2:c.65A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166176.2:c.65A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004387.4:c.65A>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000925201Stanford Center for Inherited Cardiovascular Disease, Stanford University
no assertion criteria provided
Uncertain significance
(Nov 6, 2017) 		germlineprovider interpretation

SCV002501129AiLife Diagnostics, AiLife Diagnostics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 18, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedprovider interpretation
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

NKX2.5 mutations in patients with congenital heart disease.

McElhinney DB, Geiger E, Blinder J, Benson DW, Goldmuntz E.

J Am Coll Cardiol. 2003 Nov 5;42(9):1650-5.

PubMed [citation]
PMID:
14607454

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Stanford Center for Inherited Cardiovascular Disease, Stanford University, SCV000925201.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedprovider interpretationnot provided

Description

p.Gln22Pro ( c.65A>C) in exon 1 of the NKX2-5 gene (NM_004387.3; chr5-172662022-T-G) SCICD Classification: variant of uncertain significance based on limited data to associate this gene with disease, lack of case data and sufficiently rare. We do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). We have seen this variant in a family with arrhythmic cardiomyopathy (DCM/ARVC). Population data: Highest MAF in Latino population: 0.002987% (gnomAD 1/16742). GnomAD overall: 1/119469 individuals. The Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. Another variant at the same codon, p.Gln22Arg has been seen in gnomAD with an MAF of 0.02230% in non-Finnish Europeans (27/60546 individuals).

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

From AiLife Diagnostics, AiLife Diagnostics, SCV002501129.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: May 1, 2024