6-51753281-A-G
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_138694.4(PKHD1):c.8870T>C(p.Ile2957Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000675 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2957M) has been classified as Likely pathogenic.
Frequency
Consequence
NM_138694.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.8870T>C | p.Ile2957Thr | missense_variant | 57/67 | ENST00000371117.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.8870T>C | p.Ile2957Thr | missense_variant | 57/67 | 1 | NM_138694.4 | P2 | |
PKHD1 | ENST00000340994.4 | c.8870T>C | p.Ile2957Thr | missense_variant | 57/61 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251136Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135702
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461540Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727076
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
Autosomal recessive polycystic kidney disease Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 23, 2017 | Variant summary: The PKHD1 c.8870T>C (p.Ile2957Thr) variant involves the alteration of a conserved nucleotide, which 3/4 in silico tools predict damaging outcome for this variant. This variant was found in 10/122220 control chromosomes at a frequency of 0.0000818, which does not exceed the estimated maximal expected allele frequency of a pathogenic PKHD1 variant (0.0070711). In literature, this variant is widely reported as a pathogenic variant and is found in several patients with autosomal recessive polycystic kidney disease with consistent genotype-phenotype evidences. Available patient data show that this variant is a severe mutation. A patient who carried 10627delT and p.I2957T variants was found to have no ARPKD protein (i.e. fibronectin), strongly suggesting that this variant leads to functional impairment (Ward_2003). Multiple clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 2957 of the PKHD1 protein (p.Ile2957Thr). This variant is present in population databases (rs760222236, gnomAD 0.01%). This missense change has been observed in individual(s) with polycystic kidney disease (PMID: 11898128, 11919560, 12506140, 15698423, 15805161, 19914852, 27225849). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 357423). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PKHD1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | Across nine studies, the PKHD1 c.8870T>C (p.Ile2957Thr) missense variant is reported in a total of 23 patients, including 19 compound heterozygotes with autosomal recessive polycystic kidney disease (ARPKD), one compound heterozygote with Caroli's disease and congenital hepatic fibrosis with minimal kidney involvement, two ARPKD patients carrying three variants in the PKHD1 gene, and one heterozygote in whom a second variant was not identified (Onuchic et al. 2002; Ward et al. 2002; Bergmann et al. 2003; Rossetti et al. 2003; Sharp et al. 2005; Gunay-Aygun et al. 2010; Denamur et al. 2010; Brinkert et al. 2013; Melchionda et al. 2016). Additionally, the p.Ile2957Thr variant was found in a heterozygous state in three unaffected family members of patients, and is noted to segregate in a manner consistent with recessive inheritance. The variant was absent from 360 control individuals and from at least 300 control chromosomes, but is reported at a frequency of 0.00013 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence, the p.Ile2957Thr variant is classified as pathogenic for autosomal recessive polycystic kidney disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Mar 17, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Polycystic kidney disease 4 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 11, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 28, 2024 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Jul 17, 2023 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with polycystic kidney disease 4, with or without hepatic disease (MIM#263200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. There is significant intrafamilial variation of severity (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to threonine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (15 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0704 - Another missense variant comparable to the one identified in this case has limited previous evidence for pathogenicity. This alternative change (p.(Ile2957Met)) has been reported as likely pathogenic (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic, and observed in compound heterozygous individuals with polycystic kidney disease, and once in an individual with congenital hepatic fibrosis (ClinVar). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Polycystic kidney disease Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The PKHD1 p.Ile2957Thr variant was identified in 15 of 690 proband chromosomes (frequency: 0.02) from individuals or families with ARPKD or congenital hepatic fibrosis and was not identified in 520 chromosomes from healthy individuals (Adeva 2006, Denamur 2010, Furu 2003, Gunay-Aygun 2010, Sharp 2005, Ward 2002). The variant was also identified in dbSNP (ID: rs760222236) “With Pathogenic allele”, ClinVar (classified pathogenic by Illumina Clinical Services Laboratory), RWTH AAachen University ARPKD database (classified pathogenic). The variant was also identified in control databases in 16 of 276840 chromosomes at a frequency of 0.00006 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 1 of 24028 chromosomes (freq: 0.00004), European Non-Finnish in 14 of 126434 chromosomes (freq: 0.0001), and South Asian in 1 of 30782 chromosomes (freq: 0.00003); it was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, or European Finnish populations. The p.Ile2957 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Thr variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 20413436, 12846734, 19914852, 12874454, 15805161, 25701400, 15108281, 12506140, 27225849, 26385851, 11919560, 11898128, 19940839, 31980526, 32571524, 32574212, 31589614, 32939031) - |
PKHD1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 02, 2024 | The PKHD1 c.8870T>C variant is predicted to result in the amino acid substitution p.Ile2957Thr. This variant has been widely reported to be pathogenic for autosomal recessive polycystic kidney disease (ARPKD) (see for example, Ward et al. 2002. PubMed ID: 11919560; Obeidova et al. 2020. PubMed ID: 32574212; Table S2, Jayasinghe et al. 2021. PubMed ID: 32939031). This variant is reported in 0.010% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at