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NM_001009944.3(PKD1):c.971G>T (p.Arg324Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Aug 17, 2021)
Last evaluated:
Sep 15, 2020
Accession:
VCV000008205.16
Variation ID:
8205
Description:
single nucleotide variant
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NM_001009944.3(PKD1):c.971G>T (p.Arg324Leu)

Allele ID
23244
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2118021 (GRCh38) GRCh38 UCSC
16: 2168022 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P98161:p.Arg324Leu
NC_000016.10:g.2118021C>A
NC_000016.9:g.2168022C>A
... more HGVS
Protein change
R324L
Other names
-
Canonical SPDI
NC_000016.10:2118020:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00274
The Genome Aggregation Database (gnomAD) 0.00351
Trans-Omics for Precision Medicine (TOPMed) 0.00252
The Genome Aggregation Database (gnomAD) 0.00480
Links
ClinGen: CA119379
UniProtKB: P98161#VAR_010085
OMIM: 601313.0011
dbSNP: rs199476099
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Apr 19, 2019 RCV000008688.7
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 15, 2020 RCV000756490.6
Benign 1 no assertion criteria provided - RCV001292035.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PKD1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1834 2184

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 19, 2019)
criteria provided, single submitter
Method: clinical testing
Polycystic kidney disease, adult type
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884320.2
Submitted: (Aug 05, 2019)
Evidence details
Uncertain significance
(Jan 01, 2016)
criteria provided, single submitter
Method: clinical testing
Polycystic kidney disease, adult type
Allele origin: unknown
Centre for Mendelian Genomics,University Medical Centre Ljubljana
Accession: SCV001370129.2
Submitted: (Nov 24, 2020)
Evidence details
Comment:
This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PS1,PP3,PP4,BP6,BS2.
Likely benign
(Sep 15, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001791088.1
Submitted: (Aug 17, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 10364515, 12662927, 27499327, 19759016, 21115670, 17582161)
Likely pathogenic
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001150735.7
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Jul 01, 1999)
no assertion criteria provided
Method: literature only
POLYCYSTIC KIDNEY DISEASE 1
Allele origin: germline
OMIM
Accession: SCV000028897.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jan 06, 2020)
no assertion criteria provided
Method: curation
Polycystic kidney disease, adult type
Allele origin: germline
Reproductive Health Research and Development,BGI Genomics
Accession: SCV001142453.1
Submitted: (Jan 06, 2020)
Evidence details
Comment:
NM_001009944.2:c.971G>T in the PKD1 gene has an allele frequency of 0.006 in European (Finnish) subpopulation in the gnomAD database. This variant has been detected in … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
Polycystic Kidney disease
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001480652.1
Submitted: (Feb 03, 2021)
Evidence details
Comment:
The PKD1 p.Arg324Leu variant was identified in 6 of 720 proband chromosomes (frequency: 0.008) from individuals or families with ADPKD (Thomas 1999, Hoefele 2011, Rossetti … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene, PKD1, by long-range PCR. Thomas R American journal of human genetics 1999 PMID: 10364515

Text-mined citations for rs199476099...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021