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NM_001079668.3(NKX2-1):c.915del (p.Ala306fs) AND NKX2-1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 10, 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:
RCV004545662.1

Allele description

NM_001079668.3(NKX2-1):c.915del (p.Ala306fs)

Genes:
NKX2-1:NK2 homeobox 1 [Gene - OMIM - HGNC]
SFTA3:surfactant associated 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q13.3
Genomic location:
Preferred name:
NM_001079668.3(NKX2-1):c.915del (p.Ala306fs)
HGVS:
  • NC_000014.9:g.36517573del
  • NG_013365.1:g.7657del
  • NG_128910.1:g.183del
  • NM_001079668.3:c.915delMANE SELECT
  • NM_003317.4:c.825del
  • NP_001073136.1:p.Ala306fs
  • NP_003308.1:p.Ala276fs
  • NC_000014.8:g.36986778del
  • NM_001079668.2:c.915delC
Protein change:
A276fs
Molecular consequence:
  • NM_001079668.3:c.915del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003317.4:c.825del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
NKX2-1-related disorder
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004777189PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Dec 10, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 PreventionGenetics, part of Exact Sciences, SCV004777189.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The NKX2-1 c.915delC variant is predicted to result in a frameshift and premature protein termination (p.Ala306Argfs*75). This variant (also reported as 825delC, Ala276Argfs*75) was reported in individuals with hypothyroidism and chorea (Moya et al. 2006. PubMed ID: 16507635; Moya et al. 2018. PubMed ID: 29294041). Functional studies also indicate this variant results in a protein which acts in a dominant negative manner (Moya et al. 2006. PubMed ID: 16507635). This variant has not been reported in a large population database, indicating this variant is rare. Frameshift variants in NKX2-1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Sep 29, 2024