NM_001079668.3(NKX2-1):c.464-2A>T AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 17, 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:: RCV002512944.3

Allele description [Variation Report for NM_001079668.3(NKX2-1):c.464-2A>T]

NM_001079668.3(NKX2-1):c.464-2A>T

Genes:

NKX2-1:NK2 homeobox 1 [Gene - OMIM - HGNC]
SFTA3:surfactant associated 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q13.3

Genomic location:

Preferred name:

NM_001079668.3(NKX2-1):c.464-2A>T

HGVS:

NC_000014.9:g.36518022T>A
NG_013365.1:g.7204A>T
NG_128910.1:g.632T>A
NM_001079668.3:c.464-2A>TMANE SELECT
NM_003317.4:c.374-2A>T
NC_000014.8:g.36987227T>A
NM_001079668.2:c.464-2A>T

Note:

NCBI staff reviewed the sequence information reported in PubMed 12891678 Fig. 3a to determine the location of this allele on the current reference sequence.

Nucleotide change:

IVS2AS, A-T, -2

Links:

OMIM: 600635.0007; dbSNP: rs587776708

NCBI 1000 Genomes Browser:

rs587776708

Molecular consequence:

NM_001079668.3:c.464-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_003317.4:c.374-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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tripartite motif-containing 45 [Homo sapiens]
tripartite motif-containing 45 [Homo sapiens]
gi|13376780|ref|NP_079464.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003442331	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 17, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 17576681, 9536098, 12891678, 15289765, 24930029, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003442331

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 17, 2023)

germline

clinical testing

PubMed (6)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003442331.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 8978). This variant is also known as -2A>T substitution in the invariant AG splice acceptor site of intron 2. Disruption of this splice site has been observed in individual(s) with clinical features of NKX2-1-related conditions (PMID: 12891678, 15289765, 24930029). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 2 of the NKX2-1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.

#	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: Sep 29, 2024

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