12-95483273-G-T

Position:

• chr12-95483273-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006838.4(METAP2):​c.318G>T​(p.Lys106Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: METAP2 NM_006838.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.71

Genes affected

METAP2 (HGNC:16672): (methionyl aminopeptidase 2) The protein encoded by this gene is a member of the methionyl aminopeptidase family. The encoded protein functions both by protecting the alpha subunit of eukaryotic initiation factor 2 from inhibitory phosphorylation and by removing the amino-terminal methionine residue from nascent proteins. Increased expression of this gene is associated with various forms of cancer, and the anti-cancer drugs fumagillin and ovalicin inhibit the protein by irreversibly binding to its active site. Inhibitors of this gene have also been shown to be effective for the treatment of obesity. A pseudogene of this gene is located on chromosome 2. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

METAP2 (HGNC:):

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=0.22538707).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
METAP2	NM_006838.4	c.318G>T	p.Lys106Asn	missense_variant	3/11	ENST00000323666.10	NP_006829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
METAP2	ENST00000323666.10	c.318G>T	p.Lys106Asn	missense_variant	3/11	1	NM_006838.4	ENSP00000325312.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 22, 2023

The c.318G>T (p.K106N) alteration is located in exon 3 (coding exon 3) of the METAP2 gene. This alteration results from a G to T substitution at nucleotide position 318, causing the lysine (K) at amino acid position 106 to be replaced by an asparagine (N). 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	Uncertain	0.45
BayesDel_addAF	Uncertain	0.057	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.58	D;.;.;T;T;T
Eigen	Benign	-0.0020
Eigen_PC	Benign	0.082
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.93	D;T;D;D;D;D
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.23	T;T;T;T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Uncertain	2.3	M;M;.;.;.;.
PrimateAI	Uncertain	0.73	T
PROVEAN	Uncertain	-2.9	D;N;N;D;N;D
REVEL	Benign	0.10
Sift	Uncertain	0.013	D;D;D;T;T;D
Sift4G	Benign	0.068	T;T;T;T;T;T
Polyphen		0.32	B;.;.;.;P;B
Vest4		0.49
MutPred		0.31		Loss of methylation at K106 (P = 2e-04);Loss of methylation at K106 (P = 2e-04);.;.;.;.;
MVP		0.21
MPC		1.1
ClinPred		0.97	D
GERP RS		4.1
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		3.9
Varity_R		0.21
gMVP		0.38

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

Other links and lift over

dbSNP: rs2076172007; hg19: chr12-95877049;