19-51380516-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001161748.2(LIM2):c.449C>T(p.Thr150Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000173 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
LIM2
NM_001161748.2 missense
NM_001161748.2 missense
Scores
6
9
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.10
Genes affected
LIM2 (HGNC:6610): (lens intrinsic membrane protein 2) This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataractogenesis. Mutations in this gene have been associated with cataract formation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.872
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIM2 | NM_001161748.2 | c.449C>T | p.Thr150Met | missense_variant | 4/5 | ENST00000596399.2 | |
LIM2 | NM_030657.4 | c.575C>T | p.Thr192Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIM2 | ENST00000596399.2 | c.449C>T | p.Thr150Met | missense_variant | 4/5 | 1 | NM_001161748.2 | P1 | |
LIM2 | ENST00000221973.7 | c.575C>T | p.Thr192Met | missense_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251378Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135868
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GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461886Hom.: 0 Cov.: 38 AF XY: 0.0000138 AC XY: 10AN XY: 727244
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74308
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.
REVEL
Pathogenic
Sift
Uncertain
D;.
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
0.71
.;Loss of glycosylation at T150 (P = 0.1068);
MVP
MPC
ClinPred
D
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at