PMC

Human NPHP4 cDNA sequence and deduced nephroretinin amino acid sequence. Exons are numbered at right. Exon sequence alternates in color. Start codon, stop codon, and the variant polyadenylation signal AACAAA are underlined.

Alignment of human, mouse, and C. elegans deduced nephroretinin sequences. The order from top to bottom is human, mouse, and C. elegans ( accession numbers BankIt 486643, BankIt 486675, and Z81579, respectively). Identities are shown in reverse (white on black), and similarities between all three sequences are shown on gray background. There was 82% amino acid identity between human and mouse sequences and 23% amino acid identity between human and C. elegans sequences. Boxes above the sequence delimit motifs as predicted by the programs given in parenthesis: NLS = nuclear localization domain (); ER = endoplasmic reticulum membrane domain (); E-rich = glutamic acid–rich domain (); S-rich = serine-rich domain (); P-rich = proline-rich domain (); and DUF339 = PFAM (protein families database of alignments) domain of unknown function (). In H. salinarium, the program detected a 30% sequence identity with gas-vesicle protein gvpL of H. salinarium ( accession number P33964).

Northern blot analysis of the NPHP4 expression pattern. A multiple-tissue northern blot with human adult poly(A)⁺ RNA was hybridized with a 584-bp NPHP4 human DNA probe. Expression of a 5.0-kb transcript (arrowhead) is apparent in all tissues studied, with highest expression being in skeletal muscle.

Positional cloning strategy for the NPHP4 gene, on human chromosome 1p36. A, Genetic map position for microsatellites used in linkage mapping of NPHP4 (see ). Sex-averaged genetic distance (in cM) from the map was used. Published flanking markers are underlined (Schuermann et al. ). p-ter = Telomeric; cen = centromeric. B, Physical map distances of critical microsatellites relative to D1S2660. The secure 1.2-Mb critical interval (solid bar) and the 700-kb suggestive critical interval (stippled bar) are delimited by the newly identified secure flanking markers (asterisks) and suggestive flanking markers (double asterisks) defined by haplotype analysis (see ). Below the axis, known genes (green), predicted unknown genes (blue), and the NPHP4 gene (also known as “Q9UFQ2”) are represented as arrows in the direction of transcription. C, Genomic organization of NPHP4, with exons indicated by vertical hatches and numbered. D, Exon structure of NPHP4 cDNA. Blackened and unblackened boxes represent the 30 exons encoding nephroretinin. The number of the first codon of each exon is indicated; exons beginning with the second or third base of a codon are indicated by “b” or “c,” respectively. At bottom, locations of the 11 different mutations identified in eight kindreds with NPHP4 mutations are shown. fs = Frameshift. E, NPHP4 mutations occurring homozygously in affected individuals from five consanguineous families (underlined). Compound heterozygous mutations are not shown. Mutated nucleotides and altered amino acids are depicted on gray background.