ENST00000256644.8:c.118G>C

Variant summary

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

The ENST00000256644.8(LAMTOR5):​c.118G>C​(p.Val40Leu) 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. 12/16 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. V40M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

LAMTOR5
ENST00000256644.8 missense

Scores

1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.682
Variant links:
Genes affected
LAMTOR5 (HGNC:17955): (late endosomal/lysosomal adaptor, MAPK and MTOR activator 5) This gene encodes a protein that specifically complexes with the C-terminus of hepatitis B virus X protein (HBx). The function of this protein is to negatively regulate HBx activity and thus to alter the replication life cycle of the virus. [provided by RefSeq, Jul 2008]
LAMTOR5-AS1 (HGNC:40823): (LAMTOR5 and SLC16A4 antisense RNA 1)

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=0.10070342).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LAMTOR5NM_006402.3 linkc.118G>C p.Val40Leu missense_variant Exon 1 of 4 NP_006393.2 O43504A0A8Z5A536

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LAMTOR5ENST00000256644.8 linkc.118G>C p.Val40Leu missense_variant Exon 1 of 4 1 ENSP00000256644.4 A0A8Z5A536
LAMTOR5-AS1ENST00000457535.6 linkn.225C>G non_coding_transcript_exon_variant Exon 1 of 3 3
LAMTOR5-AS1ENST00000625451.2 linkn.122C>G non_coding_transcript_exon_variant Exon 1 of 4 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
3.0
DANN
Benign
0.82
Eigen
Benign
-0.72
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.39
.;T
M_CAP
Benign
0.0025
T
MetaRNN
Benign
0.10
T;T
MetaSVM
Benign
-0.97
T
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.090
N;.
REVEL
Benign
0.0070
Sift
Benign
0.042
D;.
Sift4G
Pathogenic
0.0
D;D
Vest4
0.061
MutPred
0.25
Loss of catalytic residue at V40 (P = 0.1171);Loss of catalytic residue at V40 (P = 0.1171);
MVP
0.41
MPC
0.23
ClinPred
0.088
T
GERP RS
-1.7
gMVP
0.084

Splicing

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: rs779697012; hg19: chr1-110950371; API