Variant chr19-48491505-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001388485.1(LMTK3):c.4127C>G(p.Pro1376Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 8.0e-7 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LMTK3
NM_001388485.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.691

Variant links:

Genes affected

LMTK3 (HGNC:19295): (lemur tyrosine kinase 3) Predicted to enable protein kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in Golgi membrane; axon; and dendrite. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LMTK3 links:

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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=0.22580826).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
LMTK3	NM_001388485.1 linkuse as main transcript	c.4127C>G	p.Pro1376Arg	missense_variant	13/15	ENST00000600059.6
LMTK3	NM_001080434.2 linkuse as main transcript	c.4127C>G	p.Pro1376Arg	missense_variant	14/16
LMTK3	XM_011526411.3 linkuse as main transcript	c.4205C>G	p.Pro1402Arg	missense_variant	14/16
LMTK3	XM_011526412.3 linkuse as main transcript	c.4172C>G	p.Pro1391Arg	missense_variant	14/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMTK3	ENST00000600059.6 linkuse as main transcript	c.4127C>G	p.Pro1376Arg	missense_variant	13/15	2	NM_001388485.1	P2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

7.96e-7

AC:

AN:

1256610

Hom.:

Cov.:

AF XY:

0.00000164

AC XY:

AN XY:

610888

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:

9.90e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000227

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

Aug 12, 2021

The c.4214C>G (p.P1405R) alteration is located in exon 14 (coding exon 14) of the LMTK3 gene. This alteration results from a C to G substitution at nucleotide position 4214, causing the proline (P) at amino acid position 1405 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.097

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0060

T;.;.

Eigen

Benign

-0.084

Eigen_PC

Benign

0.020

FATHMM_MKL

Benign

0.59

LIST_S2

Benign

0.55

T;T;T

M_CAP

Uncertain

0.21

MetaRNN

Benign

0.23

T;T;T

MetaSVM

Benign

-0.87

MutationAssessor

Benign

1.0

L;.;.

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-2.2

.;N;.

REVEL

Benign

0.21

Sift

Uncertain

0.020

.;D;.

Sift4G

Benign

0.083

T;T;.

Polyphen

0.62

P;.;.

Vest4

0.35

MutPred

0.24

Gain of solvent accessibility (P = 0.0971);.;.;

MVP

0.56

ClinPred

0.37

GERP RS

3.5

Varity_R

0.069

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over