NM_001079668.3(NKX2-1):c.(?_-1)_*(1206_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 7, 2019
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:: RCV000787032.1

Allele description [Variation Report for NM_001079668.3(NKX2-1):c.(?_-1)_*(1206_?)del]

NM_001079668.3(NKX2-1):c.(?_-1)_*(1206_?)del

Genes:

NKX2-1:NK2 homeobox 1 [Gene - OMIM - HGNC]
NKX2-1-AS1:NKX2-1 antisense RNA 1 [Gene - 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.(?_-1)_*(1206_?)del

HGVS:

NC_000014.9:g.(?_36516072)_(36520130_?)del
NC_000014.8:g.(?_36985277)_(36989335_?)del

Condition(s)

Name:: Benign hereditary chorea (BHC)
Synonyms:: HEREDITARY PROGRESSIVE CHOREA WITHOUT DEMENTIA
Identifiers:: MONDO: MONDO:0021011; MedGen: C0393584; Orphanet: 1429; OMIM: 118700

Name:: Brain-lung-thyroid syndrome
Synonyms:: Choreoathetosis, hypothyroidism, and neonatal respiratory distress; CHOREOATHETOSIS AND CONGENITAL HYPOTHYROIDISM WITH PULMONARY DYSFUNCTION
Identifiers:: MONDO: MONDO:0012593; MedGen: C1970269; Orphanet: 209905; OMIM: 610978

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000925944	Johns Hopkins Genomics, Johns Hopkins University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 7, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23430038, 24714694, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000925944

Johns Hopkins Genomics, Johns Hopkins University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 7, 2019)

germline

clinical testing

PubMed (3)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Heterogeneous pulmonary phenotypes associated with mutations in the thyroid transcription factor gene NKX2-1.

Hamvas A, Deterding RR, Wert SE, White FV, Dishop MK, Alfano DN, Halbower AC, Planer B, Stephan MJ, Uchida DA, Williames LD, Rosenfeld JA, Lebel RR, Young LR, Cole FS, Nogee LM.

Chest. 2013 Sep;144(3):794-804. doi: 10.1378/chest.12-2502.

PubMed [citation]

PMID:: 23430038
PMCID:: PMC3760742

Comprehensive genotyping and clinical characterisation reveal 27 novel NKX2-1 mutations and expand the phenotypic spectrum.

Thorwarth A, Schnittert-Hübener S, Schrumpf P, Müller I, Jyrch S, Dame C, Biebermann H, Kleinau G, Katchanov J, Schuelke M, Ebert G, Steininger A, Bönnemann C, Brockmann K, Christen HJ, Crock P, deZegher F, Griese M, Hewitt J, Ivarsson S, Hübner C, Kapelari K, et al.

J Med Genet. 2014 Jun;51(6):375-87. doi: 10.1136/jmedgenet-2013-102248. Epub 2014 Apr 8.

PubMed [citation]

PMID:: 24714694
PMCID:: PMC5240655

See all PubMed Citations (3)

Details of each submission

From Johns Hopkins Genomics, Johns Hopkins University, SCV000925944.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

Evidence of an NKX2-1 gene deletion involving all coding exons was identified. We are not able to determine the specific breakpoints of the deletion, and it may include neighboring genes. Whole NKX2-1 gene deletions have been previously reported as causes of choreoathetosis, congenital hypothyroidism, neonatal respiratory distress syndrome. Therefore, this variant is considered pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 1, 2023

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