PAGE2 p.Met68Ile

Variant names:

• chrX-55091342-G-T
• NM_207339.4:c.204G>T
• PAGE2 p.Met68Ile

Your query was ambiguous. Multiple possible variants found:

• chrX-55091342-G-T
• chrX-55091342-G-C
• chrX-55091342-G-A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_207339.4(PAGE2):​c.204G>T​(p.Met68Ile) 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. 14/20 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 21)
• Consequence: PAGE2 NM_207339.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 0 publications found

Genes affected

PAGE2 (HGNC:31804): (PAGE family member 2)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10596359).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207339.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAGE2	NM_207339.4	MANE Select	c.204G>T	p.Met68Ile	missense	Exon 4 of 5	NP_997222.1	Q7Z2X7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAGE2	ENST00000374968.9	TSL:1 MANE Select	c.204G>T	p.Met68Ile	missense	Exon 4 of 5	ENSP00000364107.4	Q7Z2X7
	PAGE2	ENST00000374965.5	TSL:2	c.153G>T	p.Met51Ile	missense	Exon 4 of 5	ENSP00000364104.1	X6R922

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.57	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.44
DEOGEN2	Benign	0.0079	T
FATHMM_MKL	Benign	0.0044	N
LIST_S2	Benign	0.65	T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.033
PROVEAN	Benign	0.29	N
REVEL	Benign	0.024
Sift	Benign	0.036	D
Sift4G	Benign	0.26	T
Varity_R		0.11
gMVP		0.012
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chrX-55117775;