Parametric linkage analysis with genome-wide SNP markers at a 2 cM interval showed a single candidate region at chromosome 5 (
Fig. 7A, upper panel). Further linkage analysis using SNP markers at a 1 cM interval revealed the maximum multipoint parametric LOD score of approximately 3.56 on chromosome 5p13.3-p13.1 with an interval delineated by markers rs13187570 and rs395967 (
Fig. 7A, lower panel). The region encompassed 7.2 Mb of length that included the
SLC45A2 gene (See
Supplementary Fig.). A novel nonsynonymous sequence change in the coding sequence of the
SLC45A2 gene was found in the proband (V:10):c.208T>C, which predicted a p.Y70H change (
Fig. 7B). Codon 70 is located in the second transmembrane domain in the highly conserved MFS/sugar transport protein region spanning codons 35 to 524 (db_xref, CDD: 257676;
Fig. 7C). This heterozygous variant was found in all of the affected patients, indicating that the variant cosegregated with the disease. The p.Y70H variant was not found in the Human Gene Mutation Database (available in the public domain at
http://www.hgmd.cf.ac.uk), the dbSNP database (available in the public domain at
http://www.ncbi.nlm.nih.gov/projects/SNP/), the 1000 Genomes Project (available in the public domain at
http://www.1000genomes.org/), or in the NHLBI Exome Sequencing Project (available in the public domain at
http://evs.gs.washington.edu/EVS/). We used the Human Genome Variation Database (available in the public domain at
http://www.hgvd.genome.med.kyoto-u.ac.jp/), which contains the genetic variations determined by exome sequencing of 1208 Japanese individuals, instead of performing sequencing in human controls; however, the variant was not found. Computational analyses indicated that p.Y70H was “possibly damaging,” with a score of 0.950 by PolyPhen-2; “damaging,” with a score of 0.013 by SIFT; “deleterious,” with a score of −2.93 by PROVEAN; and “disease-causing,” with a score of 83 by MutationTaster. The c.208T>C change is considered to be a “likely pathogenic variant with moderate evidence of pathogenicity” according to the latest American College of Medical Genetics (ACMG) standards and guidelines for the interpretation of sequence variants (see
Supplementary Table for the pathogenicity based on the ACMG guidelines).
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