18-2554759-C-A

Variant summary

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

The NM_022840.5(METTL4):​c.739G>T​(p.Val247Leu) 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. 15/21 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)

Consequence

METTL4
NM_022840.5 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.733
Variant links:
Genes affected
METTL4 (HGNC:24726): (methyltransferase 4, N6-adenosine) Enables RNA methyltransferase activity and site-specific DNA-methyltransferase (adenine-specific) activity. Involved in nucleic acid metabolic process; regulation of RNA metabolic process; and regulation of mitochondrial DNA replication. Located in cytosol; mitochondrial matrix; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.07548204).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
METTL4NM_022840.5 linkuse as main transcriptc.739G>T p.Val247Leu missense_variant 4/9 ENST00000574538.2 NP_073751.3 Q8N3J2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
METTL4ENST00000574538.2 linkuse as main transcriptc.739G>T p.Val247Leu missense_variant 4/91 NM_022840.5 ENSP00000458290.1 Q8N3J2
METTL4ENST00000573134.1 linkuse as main transcriptn.1136G>T non_coding_transcript_exon_variant 3/71
METTL4ENST00000319888.10 linkuse as main transcriptc.739G>T p.Val247Leu missense_variant 4/85 ENSP00000320349.6 J3KNJ7
METTL4ENST00000577166.5 linkuse as main transcriptc.*27G>T downstream_gene_variant 4 ENSP00000458415.1 I3L0Y1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

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 submitterclinical testingAmbry GeneticsAug 02, 2021The c.739G>T (p.V247L) alteration is located in exon 4 (coding exon 3) of the METTL4 gene. This alteration results from a G to T substitution at nucleotide position 739, causing the valine (V) at amino acid position 247 to be replaced by a leucine (L). 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
0.099
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
14
DANN
Benign
0.96
DEOGEN2
Benign
0.0032
.;T
Eigen
Benign
-0.64
Eigen_PC
Benign
-0.43
FATHMM_MKL
Benign
0.71
D
LIST_S2
Benign
0.69
T;T
M_CAP
Benign
0.0039
T
MetaRNN
Benign
0.075
T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.90
.;L
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.65
N;.
REVEL
Benign
0.030
Sift
Benign
0.15
T;.
Sift4G
Benign
0.33
T;T
Polyphen
0.0020
.;B
Vest4
0.10
MutPred
0.41
Loss of catalytic residue at V247 (P = 0.0098);Loss of catalytic residue at V247 (P = 0.0098);
MVP
0.23
MPC
0.094
ClinPred
0.19
T
GERP RS
3.5
Varity_R
0.045
gMVP
0.19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-2554758; API