rs149151043

Positions:

chr16-2103617-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001009944.3(PKD1):c.8440G>A(p.Gly2814Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00735 in 1,610,450 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0062 ( 5 hom., cov: 31)

Exomes 𝑓: 0.0075 ( 57 hom. )

Consequence

PKD1
NM_001009944.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 1.55

Variant links:

Genes affected

PKD1 (HGNC:9008): (polycystin 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]

PKD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0081606805).

BP6

Variant 16-2103617-C-T is Benign according to our data. Variant chr16-2103617-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 257021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2103617-C-T is described in Lovd as [Benign]. Variant chr16-2103617-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0062 (944/152302) while in subpopulation NFE AF= 0.00859 (584/68018). AF 95% confidence interval is 0.00801. There are 5 homozygotes in gnomad4. There are 495 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 944 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD1	NM_001009944.3 linkuse as main transcript	c.8440G>A	p.Gly2814Arg	missense_variant	23/46	ENST00000262304.9	NP_001009944.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1	ENST00000262304.9 linkuse as main transcript	c.8440G>A	p.Gly2814Arg	missense_variant	23/46	1	NM_001009944.3	ENSP00000262304	P5	P98161-1

Frequencies

GnomAD3 genomes

AF:

0.00621

AC:

945

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00720

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00858

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00611

AC:

1520

AN:

248758

Hom.:

AF XY:

0.00605

AC XY:

818

AN XY:

135268

show subpopulations

Gnomad AFR exome

AF:

0.00163

Gnomad AMR exome

AF:

0.00417

Gnomad ASJ exome

AF:

0.000401

Gnomad EAS exome

AF:

0.000491

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.0175

Gnomad NFE exome

AF:

0.00818

Gnomad OTH exome

AF:

0.00659

GnomAD4 exome

AF:

0.00747

AC:

10891

AN:

1458148

Hom.:

Cov.:

AF XY:

0.00714

AC XY:

5178

AN XY:

725392

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00490

Gnomad4 ASJ exome

AF:

0.000421

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.000197

Gnomad4 FIN exome

AF:

0.0166

Gnomad4 NFE exome

AF:

0.00841

Gnomad4 OTH exome

AF:

0.00628

GnomAD4 genome

AF:

0.00620

AC:

944

AN:

152302

Hom.:

Cov.:

AF XY:

0.00665

AC XY:

495

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00719

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0171

Gnomad4 NFE

AF:

0.00859

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00445

Hom.:

Bravo

AF:

0.00544

TwinsUK

AF:

0.00836

AC:

ALSPAC

AF:

0.0106

AC:

ESP6500AA

AF:

0.00137

AC:

ESP6500EA

AF:

0.00828

AC:

ExAC

AF:

0.00553

AC:

665

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2023	PKD1: BS2 -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 10, 2020	This variant is associated with the following publications: (PMID: 17574468, 12007219, 24374109, 18837007) -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Polycystic kidney disease, adult type

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 26, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Sep 13, 2021	- -

Polycystic kidney disease

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

The PKD1 p.Gly2814Arg variant was identified in 29 of 1202 proband chromosomes (frequency: 0.024) from individuals or families with ADPKD (Garcia-Gonzalez 2007, Inoue 2002, Rossetti 2001, Rossetti 2002, Rossetti 2012, Tan 2008). The variant was also identified in dbSNP (ID: rs149151043) as "With other allele ", ClinVar (classified as benign by ARUP and Prevention Genetics), LOVD 3.0 (2x as benign or with unknown effect), and in ADPKD Mutation Database (likely neutral). The variant was not identified in COGR, or PKD1-LOVD databases. The variant was identified in control databases in 1715 of 275482 chromosomes (7 homozygous) at a frequency of 0.006 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 34 of 23822 chromosomes (freq: 0.0014), Other in 43 of 6430 chromosomes (freq: 0.0066), Latino in 146 of 34410 chromosomes (freq: 0.004), European in 1016 of 125388 chromosomes (freq: 0.008), Ashkenazi Jewish in 4 of 10094 chromosomes (freq: 0.00039), East Asian in 9 of 18840 chromosomes (freq: 0.00047), Finnish in 458 of 25724 chromosomes (freq: 0.017), and South Asian in 5 of 30774 chromosomes (freq: 0.00016). In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The p.Gly2814 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In addition, the variant was identified with a co-occurring pathogenic PKD1 or PKD2 variants (PKD1 p.Glu2810*, p.Ile3109fs*, c.7704-1G>T; and PKD2 p.Arg872*), increasing the likelihood that the p.Gly2814Arg variant does not have clinical significance (Garcia-Gonzalez 2007). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -

Autosomal dominant polycystic kidney disease

Benign:1

Likely benign, criteria provided, single submitter

research

Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research

Jan 01, 2019

- -

PKD1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 05, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.31

T;.

Eigen

Uncertain

0.25

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.62

T;T

MetaRNN

Benign

0.0082

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

L;L

MutationTaster

Benign

0.99

N;N

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-2.2

N;N

REVEL

Benign

0.17

Sift

Benign

0.072

T;T

Sift4G

Uncertain

0.020

D;D

Polyphen

0.99

D;D

Vest4

0.63

MutPred

0.48

Loss of catalytic residue at G2814 (P = 0.021);Loss of catalytic residue at G2814 (P = 0.021);

MVP

0.74

ClinPred

0.013

GERP RS

3.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.068

gMVP

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over