NM_006147.4(IRF6):c.154G>T (p.Glu52Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 10, 2015
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:: RCV000255193.1

Allele description [Variation Report for NM_006147.4(IRF6):c.154G>T (p.Glu52Ter)]

NM_006147.4(IRF6):c.154G>T (p.Glu52Ter)

Gene:

IRF6:interferon regulatory factor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.2

Genomic location:

Preferred name:

NM_006147.4(IRF6):c.154G>T (p.Glu52Ter)

HGVS:

NC_000001.11:g.209801260C>A
NG_007081.2:g.9875G>T
NM_001206696.2:c.-112+4687G>T
NM_006147.4:c.154G>TMANE SELECT
NP_006138.1:p.Glu52Ter
NC_000001.10:g.209974605C>A
NM_006147.3:c.154G>T

Protein change:

E52*

Links:

dbSNP: rs886039570

NCBI 1000 Genomes Browser:

rs886039570

Molecular consequence:

NM_001206696.2:c.-112+4687G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_006147.4:c.154G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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dnaJ homolog subfamily B member 6 [Thrips palmi]
dnaJ homolog subfamily B member 6 [Thrips palmi]
gi|1841826281|ref|XP_034242536.1|

Protein
nuclear receptor-binding factor 2 isoform X4 [Macaca fascicularis]
nuclear receptor-binding factor 2 isoform X4 [Macaca fascicularis]
gi|544458381|ref|XP_005565809.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000322421	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Dec 10, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000322421

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Dec 10, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000322421.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The E52X nonsense variant in the IRF6 gene has been reported previously in association with van der Woude syndrome (de Lima et al., 2009), and its presence is consistent with the diagnosis in this patient. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. E52X was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.

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

Last Updated: Apr 23, 2022

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