rs1441482246

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM1BS2_Supporting

The ENST00000262304.9(PKD1):​c.461C>T​(p.Thr154Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,311,582 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T154T) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

PKD1
ENST00000262304.9 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.242
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM1
In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in ENST00000262304.9
BS2
High AC in GnomAdExome4 at 17 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PKD1NM_001009944.3 linkuse as main transcriptc.461C>T p.Thr154Met missense_variant 4/46 ENST00000262304.9 NP_001009944.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PKD1ENST00000262304.9 linkuse as main transcriptc.461C>T p.Thr154Met missense_variant 4/461 NM_001009944.3 ENSP00000262304 P5P98161-1
PKD1ENST00000423118.5 linkuse as main transcriptc.461C>T p.Thr154Met missense_variant 4/461 ENSP00000399501 A2P98161-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000286
AC:
2
AN:
69988
Hom.:
0
AF XY:
0.0000281
AC XY:
1
AN XY:
35588
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000706
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000117
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000130
AC:
17
AN:
1311582
Hom.:
0
Cov.:
19
AF XY:
0.0000122
AC XY:
8
AN XY:
656536
show subpopulations
Gnomad4 AFR exome
AF:
0.0000324
Gnomad4 AMR exome
AF:
0.0000249
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000263
Gnomad4 SAS exome
AF:
0.0000124
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000200
Gnomad4 OTH exome
AF:
0.0000360
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsFeb 23, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.085
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
7.0
DANN
Benign
0.60
DEOGEN2
Benign
0.19
T;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.052
N
LIST_S2
Benign
0.55
T;T
M_CAP
Pathogenic
0.71
D
MetaRNN
Uncertain
0.45
T;T
MetaSVM
Benign
-0.43
T
MutationAssessor
Benign
1.9
L;L
MutationTaster
Benign
1.0
N;N
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-0.81
N;N
REVEL
Benign
0.16
Sift
Benign
0.23
T;T
Sift4G
Benign
0.27
T;T
Polyphen
0.55
P;B
Vest4
0.15
MutPred
0.40
Loss of glycosylation at T154 (P = 0.0295);Loss of glycosylation at T154 (P = 0.0295);
MVP
0.72
ClinPred
0.041
T
GERP RS
-3.5
Varity_R
0.012
gMVP
0.25

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs1441482246; hg19: chr16-2168745; API