Table 1.

Annotation, functional prediction and population frequencies of the IFT88 single nucleotide variant shared by individuals affected with cleft lip and palate

General variant information and annotation
Gene	Chr	Position (HG19)	Ref	Alt	Transcript	cDNA	Protein
IFT88	13	21175919	G	C	NM_175605.3	c.915G>C	p.E305D
Conservation and in silico predictions
GERP ++	phastCons7 way vertebrate	CADD phred	SIFT	Polyphen2	Mutation Taster score	FATHMM score	LRT rank score
5.51	0.998	22.4	0.061;0.058	0.693;0.992	0.999999	-3.62	0.84324
Allele frequencies in various populations and databases
Allele Freq 1000 genomes African populations	Allele Freq 1000 genomes American populations	Allele Freq 1000 genomes Asian populations	Allele Freq 1000 genomes European populations	Allele Freq UK 10K project	Allele Freq TWINS UK project	Allele Freq Exome Variant Server	Allele Freq ExAC
0	0	0	0	0	0	0	0.0001105