rs34192428

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005565.5(LCP2):​c.1229C>T​(p.Ser410Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S410C) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

LCP2
NM_005565.5 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04
Variant links:
Genes affected
LCP2 (HGNC:6529): (lymphocyte cytosolic protein 2) This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13995245).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LCP2NM_005565.5 linkc.1229C>T p.Ser410Phe missense_variant Exon 18 of 21 ENST00000046794.10 NP_005556.1 Q13094
LCP2XM_047417171.1 linkc.998C>T p.Ser333Phe missense_variant Exon 16 of 19 XP_047273127.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LCP2ENST00000046794.10 linkc.1229C>T p.Ser410Phe missense_variant Exon 18 of 21 1 NM_005565.5 ENSP00000046794.5 Q13094
LCP2ENST00000521416.5 linkc.614C>T p.Ser205Phe missense_variant Exon 10 of 13 2 ENSP00000428871.1 E7ESF6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000409
AC:
1
AN:
244384
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
132346
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000904
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1457650
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
724854
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
0.010
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
15
DANN
Benign
0.87
DEOGEN2
Uncertain
0.57
D;T;T
Eigen
Benign
-0.67
Eigen_PC
Benign
-0.69
FATHMM_MKL
Benign
0.14
N
LIST_S2
Benign
0.79
T;T;T
M_CAP
Benign
0.040
D
MetaRNN
Benign
0.14
T;T;T
MetaSVM
Benign
-0.28
T
MutationAssessor
Uncertain
2.0
M;.;.
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.1
N;.;N
REVEL
Benign
0.11
Sift
Uncertain
0.0060
D;.;D
Sift4G
Benign
0.18
T;T;T
Polyphen
0.021
B;.;B
Vest4
0.27
MutPred
0.28
Loss of phosphorylation at S410 (P = 0.0016);Loss of phosphorylation at S410 (P = 0.0016);.;
MVP
0.57
MPC
0.19
ClinPred
0.12
T
GERP RS
3.5
Varity_R
0.037
gMVP
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34192428; hg19: chr5-169680139; API