2-175939613-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030650.3(LNPK):c.751C>A(p.Arg251Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000687 in 1,455,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
LNPK
NM_030650.3 synonymous
NM_030650.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.05
Publications
0 publications found
Genes affected
LNPK (HGNC:21610): (lunapark, ER junction formation factor) Enables identical protein binding activity. Involved in endoplasmic reticulum tubular network maintenance and positive regulation of endoplasmic reticulum tubular network organization. Located in endoplasmic reticulum tubular network membrane and nucleoplasm. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
LNPK Gene-Disease associations (from GenCC):
- neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumInheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_030650.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LNPK | MANE Select | c.751C>A | p.Arg251Arg | synonymous | Exon 10 of 13 | NP_085153.1 | Q9C0E8-1 | ||
| LNPK | c.949C>A | p.Arg317Arg | synonymous | Exon 10 of 13 | NP_001291937.1 | Q9C0E8 | |||
| LNPK | c.844C>A | p.Arg282Arg | synonymous | Exon 11 of 14 | NP_001291938.1 | Q9C0E8-4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LNPK | TSL:1 MANE Select | c.751C>A | p.Arg251Arg | synonymous | Exon 10 of 13 | ENSP00000272748.4 | Q9C0E8-1 | ||
| LNPK | TSL:1 | c.844C>A | p.Arg282Arg | synonymous | Exon 11 of 14 | ENSP00000440905.1 | Q9C0E8-4 | ||
| LNPK | TSL:1 | c.382C>A | p.Arg128Arg | synonymous | Exon 8 of 11 | ENSP00000386237.1 | Q9C0E8-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455392Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 724232 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1455392
Hom.:
Cov.:
28
AF XY:
AC XY:
1
AN XY:
724232
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33282
American (AMR)
AF:
AC:
0
AN:
44550
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26030
East Asian (EAS)
AF:
AC:
0
AN:
39540
South Asian (SAS)
AF:
AC:
0
AN:
85582
European-Finnish (FIN)
AF:
AC:
0
AN:
53364
Middle Eastern (MID)
AF:
AC:
0
AN:
5754
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1107158
Other (OTH)
AF:
AC:
0
AN:
60132
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
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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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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