ClinVar Genomic variation as it relates to human health
NM_001009944.3(PKD1):c.2180T>C (p.Leu727Pro)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Pathogenic(7); Likely pathogenic(6); Uncertain significance(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001009944.3(PKD1):c.2180T>C (p.Leu727Pro)
Variation ID: 562302 Accession: VCV000562302.29
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 2114843 (GRCh38) [ NCBI UCSC ] 16: 2164844 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Oct 1, 2018 Sep 16, 2024 Dec 13, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001009944.3:c.2180T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001009944.3:p.Leu727Pro missense NM_000296.4:c.2180T>C NP_000287.4:p.Leu727Pro missense NC_000016.10:g.2114843A>G NC_000016.9:g.2164844A>G NG_008617.1:g.26056T>C - Protein change
- L727P
- Other names
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- Canonical SPDI
- NC_000016.10:2114842:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PKD1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
3663 | 4235 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Dec 13, 2023 | RCV000681747.22 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Mar 28, 2018 | RCV000761328.2 | |
Conflicting interpretations of pathogenicity (6) |
criteria provided, conflicting classifications
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Apr 28, 2023 | RCV001095631.14 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jan 1, 2019 | RCV001254281.2 | |
Pathogenic (1) |
no assertion criteria provided
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- | RCV001292243.3 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Sep 16, 2018)
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criteria provided, single submitter
Method: research
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not provided
Affected status: yes
Allele origin:
germline
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Gharavi Laboratory, Columbia University
Accession: SCV000809204.1
First in ClinVar: Oct 01, 2018 Last updated: Oct 01, 2018 |
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Likely pathogenic
(Jan 21, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884348.1
First in ClinVar: Oct 01, 2018 Last updated: Oct 01, 2018 |
Comment:
The PKD1 c.2180T>C; p.Leu727Pro variant (rs1616940) is reported in the literature in 27 unrelated patients with autosomal dominant polycystic kidney disease (Audrezet 2012, Carrera 2016, … (more)
The PKD1 c.2180T>C; p.Leu727Pro variant (rs1616940) is reported in the literature in 27 unrelated patients with autosomal dominant polycystic kidney disease (Audrezet 2012, Carrera 2016, Cornec-Le Gall 2013, Hoefele 2011, Rossetti 2007, Rosetti 2012, Tan 2014) and is also listed on gene-specific databases (Mayo ADPKD Mutation Database) . This variant is absent from the general population with an average of 126647 alleles reported for this genomic region (1000 Genomes Project, Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The leucine at codon 727 is highly conserved and computational algorithms (SIFT, PolyPhen2, MutationTaster) predict this variant to be damaging. Based on the above information, this variant is considered likely pathogenic. References: Mayo ADPKD Mutation Database: http://pkdb.mayo.edu/cgi-bin/v2_display_mutations.cgi?GENE=PKD1&apkd_mode=PROD Audrezet M et al. Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients. Hum Mutat. 2012 Aug;33(8):1239-50. Carrera P et al. Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). Sci Rep. 2016; 6: 30850. Cornec-Le Gall E et al. Type of PKD1 mutation influences renal outcome in ADPKD. J Am Soc Nephrol. 2013 May;24(6):1006-13. Hoefele J et al. Novel PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease (ADPKD). Nephrol Dial Transplant. 2011 Jul;26(7):2181-8. Rossetti S et al. Comprehensive molecular diagnostics in autosomal dominant polycystic kidney disease. J Am Soc Nephrol. 2007 Jul;18(7):2143-60. Rossetti S et al. Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing. J Am Soc Nephrol. 2012 May;23(5):915-33. Tan A et al. Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. J Mol Diagn. 2014 Mar;16(2):216-28. (less)
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Likely pathogenic
(Mar 28, 2018)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease 3 with or without polycystic liver disease
Affected status: yes
Allele origin:
germline
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Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota
Accession: SCV000891313.1
First in ClinVar: Mar 24, 2019 Last updated: Mar 24, 2019 |
Number of individuals with the variant: 1
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Pathogenic
(Dec 05, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV000928102.1
First in ClinVar: Jul 25, 2019 Last updated: Jul 25, 2019
Comment:
Patient analyzed with Polycystic Kidney Disease Panel
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Uncertain significance
(Feb 05, 2020)
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criteria provided, single submitter
Method: research
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Polycystic kidney disease, adult type
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
unknown
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Cavalleri Lab, Royal College of Surgeons in Ireland
Accession: SCV001251272.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
PM2, PP3, PP4, PP5
Clinical Features:
Polycystic kidney dysplasia (present)
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Likely pathogenic
(Feb 01, 2020)
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criteria provided, single submitter
Method: research
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Polycystic kidney disease, adult type
Affected status: yes
Allele origin:
germline
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Molecular Biology Laboratory, Fundació Puigvert
Study: KidneyPanel_2020
Accession: SCV001425170.1 First in ClinVar: Jan 17, 2021 Last updated: Jan 17, 2021 |
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Likely pathogenic
(Jan 01, 2019)
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criteria provided, single submitter
Method: research
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Autosomal dominant polycystic kidney disease
Affected status: yes
Allele origin:
germline
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Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research
Accession: SCV001430247.1
First in ClinVar: Aug 21, 2020 Last updated: Aug 21, 2020 |
Clinical Features:
Multiple renal cysts (present) , Renal cyst (present)
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Pathogenic
(Jun 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease, adult type
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV001752484.1
First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021
Comment:
This variant has been detected in individual(s) who were sent for testing of Renasight - kidney gene panel.
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Likely pathogenic
(Jun 17, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001762205.1
First in ClinVar: Jul 30, 2021 Last updated: Jul 30, 2021 |
Clinical Features:
Polycystic kidney disease (present)
Sex: female
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Pathogenic
(Mar 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV000843112.3
First in ClinVar: Oct 01, 2018 Last updated: Sep 19, 2021 |
Comment:
This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated … (more)
This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene (PMID: 22383692, 21115670, 27835667, 22508176, 24374109). Computational tools predict that this variant is damaging. (less)
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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease, adult type
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002518864.1
First in ClinVar: May 28, 2022 Last updated: May 28, 2022 |
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Pathogenic
(Apr 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease, adult type
Affected status: unknown
Allele origin:
inherited
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New York Genome Center
Study: PrenatalSEQ
Accession: SCV005044085.1 First in ClinVar: May 19, 2024 Last updated: May 19, 2024 |
Comment:
The inherited c.2180T>C p.(Leu727Pro) variant in PKD1 has been reported in the literature in multiple individuals with polycystic kidney disease 1 [PMID: 23431072, 24374109, 29038287, … (more)
The inherited c.2180T>C p.(Leu727Pro) variant in PKD1 has been reported in the literature in multiple individuals with polycystic kidney disease 1 [PMID: 23431072, 24374109, 29038287, 30333007, 30586318, 31027891, 30816285, 33315352, 33532864, 33437033] and is listed in the Mayo Clinic Polycystic Kidney Disease variant database as Likely Pathogenic [https://pkdb.mayo.edu/variants]. The c.2180T>C variant has been deposited in ClinVar with conflicting interpretations of pathogenicity by multiple submitters, including six Pathogenic and seven Likely Pathogenic entries [ClinVar ID: 562302], and is absent from the population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. In silico predictions do not support or refute a damaging effect for p.(Leu727Pro) [CADD score = 24.6, REVEL score = 0.422]. Two other missense variants, p.(Leu727Gln) and p.(Leu727Arg), have also been listed as likely pathogenic in the Mayo Clinic Polycystic Kidney Disease variant database. Based on available evidence, the inherited heterozygous c.2180T>C p.(Leu727Pro) variant identified in PKD1 is classified as Pathogenic. (less)
Clinical Features:
Abnormal hand morphology (present) , Finger joint contracture (present)
Age: 20-29 weeks gestation
Secondary finding: yes
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Pathogenic
(Feb 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease, adult type
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557248.2
First in ClinVar: Aug 04, 2022 Last updated: Jul 23, 2024 |
Comment:
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 … (more)
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 1 (MIM#173900). (I) 0107 - This gene is associated with autosomal dominant disease. Polycystic kidney disease 1 (MIM#173900) is predominantly caused by monoallelic variants, with rare reports of biallelic variants causing disease (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from leucine to proline. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been described as pathogenic in ClinVar and the Autosomal Dominant Polycystic Kidney Disease (ADPKD) Database (PKDB). It has been reported in multiple individuals with ADPKD in the literature (PMID: 22508176; 24374109). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Likely pathogenic
(Dec 13, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001985347.4
First in ClinVar: Nov 05, 2021 Last updated: Sep 16, 2024 |
Comment:
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; … (more)
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: 26661679, 24374109, 23431072, 22090377, 17582161, 30333007, 25333066, 25646624, 27499327, 22508176, 21115670, 22383692, 29038287, 30816285, 33454723, 33437033, 33532864, 27835667, 30586318, 31027891, 36699011) (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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Polycystic Kidney disease
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001480597.1 First in ClinVar: Feb 20, 2021 Last updated: Feb 20, 2021 |
Comment:
The PKD1 p.Leu727Pro variant was identified in 19 of 3592 proband chromosomes (frequency: 0.005) from German, French, North American, Spanish, Italian and Japanese individuals or … (more)
The PKD1 p.Leu727Pro variant was identified in 19 of 3592 proband chromosomes (frequency: 0.005) from German, French, North American, Spanish, Italian and Japanese individuals or families with ADPKD, and was not identified in 480 control chromosomes from healthy individuals (Hoefele 2011, Audrézet 2012, Rossetti 2012, Hwang 2016, Trujillano 2014, Carrera 2016, Kinoshita 2016). The variant was also identified in dbSNP (ID: rs1616940), ADPKD Mutation Database (classified as Highly Likely Pathogenic), PKD1-LOVD 3.0 (classification by in silico as affecting protein function) and Clinvitae (1X). The variant was not identified in NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (March 14, 2016), the Genome Aggregation Consortium, ClinVar, COGR, MutDB and PKD1-LOVD. The p.Leu727 residue is conserved across mammals and other organisms, and 5 of 5 computational analyses programs (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant is located within a functional domain, the polycystin cation channel, increasing the likelihood that it could have clinical significance. This variant was identified in 2 individuals by our laboratory one young individual with cystic kidney disease and another under the age of 35 with bilateral multicystic kidney disease, hepatic cysts and a family history of ADPKD, increasing the likelihood it may have clinical significance. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. (less)
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Likely pathogenic
(Jan 01, 2019)
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Flagged submission
flagged submission
Method: clinical testing
Reason: This record appears to be redundant with a more recent record from the same submitter.
Notes: SCV001422364 appears to be redundant with SCV001430247.
(less)
Notes: SCV001422364 appears to
(...more)
Source: NCBI
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not provided
Affected status: yes
Allele origin:
germline
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Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research
Accession: SCV001422364.1
First in ClinVar: Jul 19, 2020 Last updated: Jul 19, 2020 |
Number of individuals with the variant: 2
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Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Clinical utility of genetic testing in early-onset kidney disease: seven genes are the main players. | Domingo-Gallego A | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2022 | PMID: 33532864 |
Genomic diagnostics in polycystic kidney disease: an assessment of real-world use of whole-genome sequencing. | Mallawaarachchi AC | European journal of human genetics : EJHG | 2021 | PMID: 33437033 |
Demographic and clinical characteristics of children with autosomal dominant polycystic kidney disease: a single center experience. | Kasap Demir B | Turkish journal of medical sciences | 2021 | PMID: 33315352 |
Value of renal gene panel diagnostics in adults waiting for kidney transplantation due to undetermined end-stage renal disease. | Ottlewski I | Kidney international | 2019 | PMID: 31027891 |
Identification of PKD1 and PKD2 gene variants in a cohort of 125 Asian Indian patients of ADPKD. | Pandita S | Journal of human genetics | 2019 | PMID: 30816285 |
Diagnostic Utility of Exome Sequencing for Kidney Disease. | Groopman EE | The New England journal of medicine | 2019 | PMID: 30586318 |
Novel mutations of PKD genes in Chinese patients suffering from autosomal dominant polycystic kidney disease and seeking assisted reproduction. | He WB | BMC medical genetics | 2018 | PMID: 30333007 |
Genetic Complexity of Autosomal Dominant Polycystic Kidney and Liver Diseases. | Cornec-Le Gall E | Journal of the American Society of Nephrology : JASN | 2018 | PMID: 29038287 |
Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System. | Kinoshita M | PloS one | 2016 | PMID: 27835667 |
Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). | Carrera P | Scientific reports | 2016 | PMID: 27499327 |
HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease. | Li S | Molecular bioSystems | 2016 | PMID: 26661679 |
An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease. | Eisenberger T | PloS one | 2015 | PMID: 25646624 |
Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing. | Trujillano D | Molecular genetics & genomic medicine | 2014 | PMID: 25333066 |
Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. | Tan AY | The Journal of molecular diagnostics : JMD | 2014 | PMID: 24374109 |
Type of PKD1 mutation influences renal outcome in ADPKD. | Cornec-Le Gall E | Journal of the American Society of Nephrology : JASN | 2013 | PMID: 23431072 |
Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients. | Audrézet MP | Human mutation | 2012 | PMID: 22508176 |
Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing. | Rossetti S | Journal of the American Society of Nephrology : JASN | 2012 | PMID: 22383692 |
Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease. | Casola C | Genome research | 2012 | PMID: 22090377 |
Novel PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease (ADPKD). | Hoefele J | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2011 | PMID: 21115670 |
Comprehensive molecular diagnostics in autosomal dominant polycystic kidney disease. | Rossetti S | Journal of the American Society of Nephrology : JASN | 2007 | PMID: 17582161 |
http://pkdb.mayo.edu | - | - | - | - |
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Text-mined citations for rs1616940 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.