Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate.
BACKGROUND
Cleft lip or palate (or the two in combination) is a common birth defect that results from a mixture of genetic and environmental factors. We searched for a specific genetic factor contributing to this complex trait by examining large numbers of affected patients and families and evaluating a specific candidate gene.


METHODS
We identified the gene that encodes interferon regulatory factor 6 (IRF6) as a candidate gene on the basis of its involvement in an autosomal dominant form of cleft lip and palate, Van der Woude's syndrome. A single-nucleotide polymorphism in this gene results in either a valine or an isoleucine at amino acid position 274 (V274I). We carried out transmission-disequilibrium testing for V274I in 8003 individual subjects in 1968 families derived from 10 populations with ancestry in Asia, Europe, and South America, haplotype and linkage analyses, and case-control analyses, and determined the risk of cleft lip or palate that is associated with genetic variation in IRF6.


RESULTS
Strong evidence of overtransmission of the valine (V) allele was found in the entire population data set (P<10(-9)); moreover, the results for some individual populations from South America and Asia were highly significant. Variation at IRF6 was responsible for 12 percent of the genetic contribution to cleft lip or palate and tripled the risk of recurrence in families that had already had one affected child.


CONCLUSIONS
DNA-sequence variants associated with IRF6 are major contributors to cleft lip, with or without cleft palate. The contribution of variants in single genes to cleft lip or palate is an important consideration in genetic counseling.
Zucchero
Theresa M
TM
University of Iowa, Iowa City 52242, USA.
Cooper
Margaret E
ME
Maher
Brion S
BS
Daack-Hirsch
Sandra
S
Nepomuceno
Buena
B
Ribeiro
Lucilene
L
Caprau
Diana
D
Christensen
Kaare
K
Suzuki
Yasushi
Y
Machida
Junichiro
J
Natsume
Nagato
N
Yoshiura
Koh-Ichiro
K
Vieira
Alexandre R
AR
Orioli
Ieda M
IM
Castilla
Eduardo E
EE
Moreno
Lina
L
Arcos-Burgos
Mauricio
M
Lidral
Andrew C
AC
Field
L Leigh
LL
Liu
You-e
YE
Ray
Ajit
A
Goldstein
Toby H
TH
Schultz
Rebecca E
RE
Shi
Min
M
Johnson
Marla K
MK
Kondo
Shinji
S
Schutte
Brian C
BC
Marazita
Mary L
ML
Murray
Jeffrey C
JC
D002971:Cleft Lip / Q000235:genetics*; D002972:Cleft Palate / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D050835:Interferon Regulatory Factors; D015810:Linkage Disequilibrium; D010375:Pedigree; D011110:Polymorphism, Genetic; D044469:Racial Groups; D012307:Risk Factors; D014157:Transcription Factors / Q000235:genetics*; D014633:Valine
D004268:DNA-Binding Proteins; C109803:IRF6 protein, human; D050835:Interferon Regulatory Factors; D014157:Transcription Factors; D014633:Valine