rs796065303
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_020376.4(PNPLA2):c.808delC(p.His270ThrfsTer50) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PNPLA2
NM_020376.4 frameshift
NM_020376.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.91
Publications
1 publications found
Genes affected
PNPLA2 (HGNC:30802): (patatin like phospholipase domain containing 2) This gene encodes an enzyme which catalyzes the first step in the hydrolysis of triglycerides in adipose tissue. Mutations in this gene are associated with neutral lipid storage disease with myopathy. [provided by RefSeq, Jul 2010]
PNPLA2 Gene-Disease associations (from GenCC):
- neutral lipid storage myopathyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-823739-GC-G is Pathogenic according to our data. Variant chr11-823739-GC-G is described in ClinVar as Pathogenic. ClinVar VariationId is 1873.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020376.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PNPLA2 | TSL:1 MANE Select | c.808delC | p.His270ThrfsTer50 | frameshift | Exon 7 of 10 | ENSP00000337701.4 | Q96AD5-1 | ||
| PNPLA2 | TSL:1 | n.96delC | non_coding_transcript_exon | Exon 2 of 4 | |||||
| PNPLA2 | c.1192delC | p.His398ThrfsTer50 | frameshift | Exon 8 of 11 | ENSP00000539342.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 221944 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
221944
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 945108Hom.: 0 Cov.: 47 AF XY: 0.00 AC XY: 0AN XY: 479484
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
945108
Hom.:
Cov.:
47
AF XY:
AC XY:
0
AN XY:
479484
African (AFR)
AF:
AC:
0
AN:
20666
American (AMR)
AF:
AC:
0
AN:
35830
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17794
East Asian (EAS)
AF:
AC:
0
AN:
25432
South Asian (SAS)
AF:
AC:
0
AN:
76706
European-Finnish (FIN)
AF:
AC:
0
AN:
36998
Middle Eastern (MID)
AF:
AC:
0
AN:
4214
European-Non Finnish (NFE)
AF:
AC:
0
AN:
689606
Other (OTH)
AF:
AC:
0
AN:
37862
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
2
-
-
Neutral lipid storage myopathy (2)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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