chr18-2931394-CAG-C
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001375808.2(LPIN2):c.1316_1317delCT(p.Ser439TrpfsTer15) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,806 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as not provided (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
LPIN2
NM_001375808.2 frameshift
NM_001375808.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.54
Publications
2 publications found
Genes affected
LPIN2 (HGNC:14450): (lipin 2) Mouse studies suggest that this gene functions during normal adipose tissue development and may play a role in human triglyceride metabolism. This gene represents a candidate gene for human lipodystrophy, characterized by loss of body fat, fatty liver, hypertriglyceridemia, and insulin resistance. [provided by RefSeq, Jul 2008]
LPIN2 Gene-Disease associations (from GenCC):
- Majeed syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 10 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;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LPIN2 | NM_001375808.2 | c.1316_1317delCT | p.Ser439TrpfsTer15 | frameshift_variant | Exon 9 of 20 | ENST00000677752.1 | NP_001362737.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457806Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 724846 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1457806
Hom.:
AF XY:
AC XY:
1
AN XY:
724846
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33430
American (AMR)
AF:
AC:
0
AN:
43954
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26014
East Asian (EAS)
AF:
AC:
1
AN:
39578
South Asian (SAS)
AF:
AC:
1
AN:
85660
European-Finnish (FIN)
AF:
AC:
0
AN:
53034
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1110132
Other (OTH)
AF:
AC:
0
AN:
60248
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Majeed syndrome Other:1
-
GeneReviews
Significance:not provided
Review Status:no classification provided
Collection Method:literature only
- -
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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