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NM_006147.4(IRF6):c.668-5T>G AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 19, 2017
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:
RCV000640126.2

Allele description [Variation Report for NM_006147.4(IRF6):c.668-5T>G]

NM_006147.4(IRF6):c.668-5T>G

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.668-5T>G
HGVS:
  • NC_000001.11:g.209790892A>C
  • NG_007081.2:g.20243T>G
  • NM_001206696.2:c.383-5T>G
  • NM_006147.4:c.668-5T>GMANE SELECT
  • NC_000001.10:g.209964237A>C
  • NM_006147.3:c.668-5T>G
Links:
dbSNP: rs1553247787
NCBI 1000 Genomes Browser:
rs1553247787
Molecular consequence:
  • NM_001206696.2:c.383-5T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006147.4:c.668-5T>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Orofacial cleft 6, susceptibility to (OFC6)
Synonyms:
CLEFT LIP WITH OR WITHOUT CLEFT PALATE, NONSYNDROMIC, 6
Identifiers:
MONDO: MONDO:0012141; MedGen: C1837213; OMIM: 608864
Name:
Popliteal pterygium syndrome (PPS)
Identifiers:
MONDO: MONDO:0017435; MedGen: C0265259
Name:
Van der Woude syndrome 1
Synonyms:
Cleft lip and/or palate with mucous cysts of lower lip
Identifiers:
MONDO: MONDO:0007333; MedGen: C4551864; OMIM: 119300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000761714Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 19, 2017) 		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 providedclinical testing

Citations

PubMed

Prevalence and nonrandom distribution of exonic mutations in interferon regulatory factor 6 in 307 families with Van der Woude syndrome and 37 families with popliteal pterygium syndrome.

de Lima RL, Hoper SA, Ghassibe M, Cooper ME, Rorick NK, Kondo S, Katz L, Marazita ML, Compton J, Bale S, Hehr U, Dixon MJ, Daack-Hirsch S, Boute O, Bayet B, Revencu N, Verellen-Dumoulin C, Vikkula M, Richieri-Costa A, Moretti-Ferreira D, Murray JC, Schutte BC.

Genet Med. 2009 Apr;11(4):241-7. doi: 10.1097/GIM.0b013e318197a49a.

PubMed [citation]
PMID:
19282774
PMCID:
PMC2789395

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000761714.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change falls in intron 6 of the IRF6 gene. It does not directly change the encoded amino acid sequence of the IRF6 protein. This variant is not present in population databases (ExAC no frequency). This variant has been reported in an individual affected with van der Woude syndrome (PMID: 19282774). This variant is also known as IVS6-5T>G in the literature. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024