ClinVar

Description

The PKHD1 p.Gly112Arg variant was identified in 1 of 328 proband chromosomes (frequency: 0.003) from individuals or families with autosomal-recessive polycystic kidney disease (ARPKD; Bergmann 2005). The variant was also identified in dbSNP (ID: rs149841071) as N/A, LOVD 3.0, RWTH AAachen University ARPKD database (classified as pathogenic). The variant was not identified in ClinVar or GeneInsight-COGR databases. The variant was identified in control databases in 95 of 277140 chromosomes at a frequency of 0.0003 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Gly112 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.