1-110406321-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001382293.1(LAMTOR5):c.94G>A(p.Gly32Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000375 in 1,600,694 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
LAMTOR5
NM_001382293.1 missense
NM_001382293.1 missense
Scores
2
7
9
Clinical Significance
Conservation
PhyloP100: 4.97
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMTOR5 | NM_001382293.1 | c.94G>A | p.Gly32Ser | missense_variant | Exon 2 of 4 | ENST00000602318.6 | NP_001369222.1 | |
LAMTOR5 | NM_006402.3 | c.340G>A | p.Gly114Ser | missense_variant | Exon 2 of 4 | NP_006393.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243944Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 132004
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GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448606Hom.: 0 Cov.: 27 AF XY: 0.00000139 AC XY: 1AN XY: 720884
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
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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 | Oct 21, 2024 | The c.340G>A (p.G114S) alteration is located in exon 2 (coding exon 2) of the LAMTOR5 gene. This alteration results from a G to A substitution at nucleotide position 340, causing the glycine (G) at amino acid position 114 to be replaced by a serine (S). 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
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;T;D;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;.;.
REVEL
Benign
Sift
Benign
T;T;.;D;.;.
Sift4G
Benign
T;T;T;D;T;D
Polyphen
0.42
.;.;B;.;.;.
Vest4
MVP
MPC
0.55
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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