ENST00000256644.8:c.118G>C

Variant names:

• chr1-110407749-C-G
• rs779697012
• ENST00000256644.8:c.118G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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)

ACMG classification

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
LAMTOR5	NM_006402.3	c.118G>C	p.Val40Leu	missense_variant	Exon 1 of 4		NP_006393.2
LAMTOR5	NM_001382293.1	c.-129G>C		upstream_gene_variant		ENST00000602318.6	NP_001369222.1
LAMTOR5-AS1	NR_102697.1	n.-60C>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMTOR5	ENST00000602318.6	c.-129G>C		upstream_gene_variant		1	NM_001382293.1	ENSP00000473439.1

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

Other links and lift over

dbSNP: rs779697012; hg19: chr1-110950371;