6-33772774-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_181336.4(LEMD2):c.1366C>T(p.Arg456Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,612,934 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
LEMD2
NM_181336.4 missense
NM_181336.4 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 3.78
Genes affected
LEMD2 (HGNC:21244): (LEM domain nuclear envelope protein 2) This gene encodes a LEM domain-containing transmembrane protein of the inner nuclear membrane. The protein is involved in nuclear structure organization and plays a role in cell signaling and differentiation. Mutations in this gene result in Cataract 46, juvenile-onset. Multiple transcript variants have been found for this gene. [provided by RefSeq, Feb 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LEMD2 | NM_181336.4 | c.1366C>T | p.Arg456Cys | missense_variant | 9/9 | ENST00000293760.10 | NP_851853.1 | |
LEMD2 | NM_001348710.2 | c.967C>T | p.Arg323Cys | missense_variant | 9/9 | NP_001335639.1 | ||
LEMD2 | NM_001143944.1 | c.460C>T | p.Arg154Cys | missense_variant | 8/8 | NP_001137416.1 | ||
LEMD2 | NM_001348709.2 | c.460C>T | p.Arg154Cys | missense_variant | 9/9 | NP_001335638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LEMD2 | ENST00000293760.10 | c.1366C>T | p.Arg456Cys | missense_variant | 9/9 | 1 | NM_181336.4 | ENSP00000293760.5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 34
GnomAD3 genomes
AF:
AC:
4
AN:
152238
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247060Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133920
GnomAD3 exomes
AF:
AC:
1
AN:
247060
Hom.:
AF XY:
AC XY:
1
AN XY:
133920
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460696Hom.: 0 Cov.: 36 AF XY: 0.00000963 AC XY: 7AN XY: 726642
GnomAD4 exome
AF:
AC:
9
AN:
1460696
Hom.:
Cov.:
36
AF XY:
AC XY:
7
AN XY:
726642
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74378
GnomAD4 genome
AF:
AC:
4
AN:
152238
Hom.:
Cov.:
34
AF XY:
AC XY:
4
AN XY:
74378
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ExAC
AF:
AC:
1
EpiCase
AF:
EpiControl
AF:
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 submitter | clinical testing | Ambry Genetics | Nov 22, 2022 | The c.1366C>T (p.R456C) alteration is located in exon 9 (coding exon 9) of the LEMD2 gene. This alteration results from a C to T substitution at nucleotide position 1366, causing the arginine (R) at amino acid position 456 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;L;.
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;.;D
REVEL
Benign
Sift
Uncertain
D;D;.;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
1.0
.;D;D;.
Vest4
0.25, 0.26, 0.27
MutPred
0.55
.;Loss of disorder (P = 0.0138);Loss of disorder (P = 0.0138);.;
MVP
MPC
1.8
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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