Identification, genomic structure, and screening of the vacuolar proton-ATPase membrane sector-associated protein M8-9 gene within the COD1 critical region (Xp11.4).
OBJECTIVE
Our goal is to identify the gene responsible for X-linked cone-rod dystrophy (COD1) that has been localized to a limited region of Xp11.4.


METHODS
A complete physical contig of the COD1 region was partially sequenced and subjected to BLAST searches to identify homologies with GenBank ESTs. ESTs were analyzed for overlapping or related cDNA sequences and retinal expression by PCR screening of multiple human retina cDNA libraries. RACE was performed to complete the missing 5' end of the transcripts. Transcripts were compared with genomic sequences to specify intron-exon boundaries. Genomic DNAs from COD1-affected males from 3 families were screened for mutations using direct PCR sequencing of the exons.


RESULTS
The vacuolar proton-ATPase membrane sector-associated protein M8-9 (APT6M8-9) gene was identified within our critical region. We confirmed its retinal expression and its genomic location in our physical contig. Eight exons (with flanking intronic sequences) were characterized from partial cDNA sequence and genomic sequence data. An additional 5' end exon was identified using RACE. No mutations were found in the COD1-affected males.


CONCLUSIONS
The combination of disease mapping and information from the Human Genome project has enabled us to identify candidate genes within the COD1 region, including APT6M8-9 gene. We found no evidence that this gene is responsible for COD1 in our families, but it may be an important candidate for other diseases that have been mapped to this region of the X chromosome.
Demirci
F Y
FY
Departments of Ophthalmology and Human Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA.
White
N J
NJ
Rigatti
B W
BW
Lewis
K F
KF
Gorin
M B
MB
D018528:ATP-Binding Cassette Transporters; D000251:Adenosine Triphosphatases / Q000235:genetics*; D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D003117:Color Vision Defects / Q000201:enzymology / Q000235:genetics; D017931:DNA Primers / Q000737:chemistry; D005091:Exons; D015723:Gene Library; D008040:Genetic Linkage; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D017494:Proton Pumps / Q000235:genetics; D006180:Proton-Translocating ATPases / Q000235:genetics*; D012174:Retinitis Pigmentosa / Q000201:enzymology / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins; D012689:Sequence Homology, Nucleic Acid; D025262:Vacuolar Proton-Translocating ATPases; D014960:X Chromosome / Q000235:genetics*
D018528:ATP-Binding Cassette Transporters; D017931:DNA Primers; D017494:Proton Pumps; C406793:SPF1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D000251:Adenosine Triphosphatases; D025262:Vacuolar Proton-Translocating ATPases; D006180:Proton-Translocating ATPases