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.
University of Iowa, Iowa City 52242, USA.
Theresa M
TM
Zucchero
Margaret E
ME
Cooper
Brion S
BS
Maher
Sandra
S
Daack-Hirsch
Buena
B
Nepomuceno
Lucilene
L
Ribeiro
Diana
D
Caprau
Kaare
K
Christensen
Yasushi
Y
Suzuki
Junichiro
J
Machida
Nagato
N
Natsume
Koh-Ichiro
K
Yoshiura
Alexandre R
AR
Vieira
Ieda M
IM
Orioli
Eduardo E
EE
Castilla
Lina
L
Moreno
Mauricio
M
Arcos-Burgos
Andrew C
AC
Lidral
L Leigh
LL
Field
You-e
YE
Liu
Ajit
A
Ray
Toby H
TH
Goldstein
Rebecca E
RE
Schultz
Min
M
Shi
Marla K
MK
Johnson
Shinji
S
Kondo
Brian C
BC
Schutte
Mary L
ML
Marazita
Jeffrey C
JC
Murray
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