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NM_001009944.3(PKD1):c.9898G>A (p.Gly3300Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 30, 2021)
Last evaluated:
Aug 12, 2021
Accession:
VCV000427112.6
Variation ID:
427112
Description:
single nucleotide variant
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NM_001009944.3(PKD1):c.9898G>A (p.Gly3300Arg)

Allele ID
415480
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2099886 (GRCh38) GRCh38 UCSC
16: 2149887 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2099886C>T
NC_000016.9:g.2149887C>T
NG_008617.1:g.43335G>A
... more HGVS
Protein change
G3300R
Other names
-
Canonical SPDI
NC_000016.10:2099885:C:T
Functional consequence
no known functional consequence
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00014
Exome Aggregation Consortium (ExAC) 0.00020
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00014
Links
ClinGen: CA7829894
dbSNP: rs777024498
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Aug 12, 2021 RCV000489976.2
Uncertain significance 1 criteria provided, single submitter May 28, 2020 RCV001171361.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 25, 2020 RCV001171380.3
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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
1832 2182

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 12, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000577744.4
Submitted: (Sep 30, 2021)
Evidence details
Comment:
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: 23431072, … (more)
Uncertain significance
(May 28, 2020)
criteria provided, single submitter
Method: research
Chronic kidney disease
(Autosomal dominant inheritance)
Allele origin: unknown
Cavalleri Lab, Royal College of Surgeons in Ireland
Accession: SCV001328308.1
Submitted: (May 28, 2020)
Evidence details
Comment:
PP3, PP5
Likely benign
(Mar 25, 2020)
criteria provided, single submitter
Method: clinical testing
Polycystic kidney disease, adult type
(Autosomal dominant inheritance)
Allele origin: germline
University of Iowa Renal Genetics Clinic,University of Iowa
Accession: SCV001250666.1
Submitted: (May 26, 2020)
Evidence details
Comment:
Segregation analysis of the Gly3300Arg variant in an unaffected family member provides evidence this variant now meets ACMG pathogenicity criteria BS4 and BP5 and is … (more)
Uncertain significance
(Jan 30, 2020)
criteria provided, single submitter
Method: clinical testing
Polycystic kidney disease, adult type
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001472254.1
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The PKD1 c.9898G>A; p.Gly3300Arg variant (rs777024498) is reported in the literature in at least one individual affected with autosomal dominant polycystic kidney disease (Cornec-Le Gall … (more)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
no known functional consequence
University of Iowa Renal Genetics Clinic,University of Iowa
Accession: SCV001250666.1
Submitted: (May 26, 2020)
Evidence details

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs777024498...

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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 20, 2021