chr4-88008021-CGAGGAGGAG-C
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3
The NM_000297.4(PKD2):c.299_307delAGGAGGAGG(p.Glu100_Glu102del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000732 in 1,366,202 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Consequence
PKD2
NM_000297.4 disruptive_inframe_deletion
NM_000297.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.36
Publications
0 publications found
Genes affected
PKD2 (HGNC:9009): (polycystin 2, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]
PKD2 Gene-Disease associations (from GenCC):
- autosomal dominant polycystic kidney diseaseInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- polycystic kidney disease 2Inheritance: AD, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_000297.4
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000297.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PKD2 | NM_000297.4 | MANE Select | c.299_307delAGGAGGAGG | p.Glu100_Glu102del | disruptive_inframe_deletion | Exon 1 of 15 | NP_000288.1 | ||
| PKD2 | NM_001440544.1 | c.299_307delAGGAGGAGG | p.Glu100_Glu102del | disruptive_inframe_deletion | Exon 1 of 14 | NP_001427473.1 | |||
| PKD2 | NR_156488.2 | n.398_406delAGGAGGAGG | non_coding_transcript_exon | Exon 1 of 14 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PKD2 | ENST00000237596.7 | TSL:1 MANE Select | c.299_307delAGGAGGAGG | p.Glu100_Glu102del | disruptive_inframe_deletion | Exon 1 of 15 | ENSP00000237596.2 | ||
| ENSG00000286618 | ENST00000662475.1 | n.112+336_112+344delCTCCTCCTC | intron | N/A | |||||
| PKD2 | ENST00000506727.1 | TSL:4 | n.-210_-202delGAGGAGGAG | upstream_gene | N/A |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 7.32e-7 AC: 1AN: 1366202Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 673980 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1366202
Hom.:
AF XY:
AC XY:
0
AN XY:
673980
show subpopulations
African (AFR)
AF:
AC:
1
AN:
30178
American (AMR)
AF:
AC:
0
AN:
33920
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24712
East Asian (EAS)
AF:
AC:
0
AN:
34472
South Asian (SAS)
AF:
AC:
0
AN:
77214
European-Finnish (FIN)
AF:
AC:
0
AN:
33704
Middle Eastern (MID)
AF:
AC:
0
AN:
5610
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1069242
Other (OTH)
AF:
AC:
0
AN:
57150
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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50-55
55-60
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Polycystic kidney disease 2 Uncertain:1
Mar 11, 2024
Fulgent Genetics, Fulgent Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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