ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8208del (p.Trp2736fs)

dbSNP: rs2151512076
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV001784842 SCV002018817 pathogenic Polycystic kidney disease 4 2019-11-18 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002541157 SCV003211908 pathogenic Autosomal recessive polycystic kidney disease 2022-06-30 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1323459). This variant has not been reported in the literature in individuals affected with PKHD1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp2736Cysfs*50) in the PKHD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PKHD1 are known to be pathogenic (PMID: 19940839).
Lifecell International Pvt. Ltd RCV001784842 SCV003925475 pathogenic Polycystic kidney disease 4 criteria provided, single submitter clinical testing A Heterozygous Frameshift variant c.8208delG in Exon 52 of the PKHD1 gene that results in the amino acid substitution p.Trp2736fs*50 was identified. The observed variant has a minimum allele frequency of 0% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic with 0 star, no assertion criteria provided (Variant ID: 1323459). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.

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