X-154031206-G-A

Variant names:

• chrX-154031206-G-A
• rs61749729
• NM_001110792.2:c.658C>T

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001110792.2(MECP2):​c.658C>T​(p.Gln220*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: MECP2 NM_001110792.2 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 5.60
• Publications: 5 publications found

Genes affected

MECP2 (HGNC:6990): (methyl-CpG binding protein 2) DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

MECP2 Gene-Disease associations (from GenCC):

• chromosome Xq28 duplication syndrome

  Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
• Rett syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
• severe neonatal-onset encephalopathy with microcephaly

  Inheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
• syndromic X-linked intellectual disability Lubs type

  Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
• atypical Rett syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• X-linked intellectual disability-psychosis-macroorchidism syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 481 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-154031206-G-A is Pathogenic according to our data. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154031206-G-A is described in CliVar as Pathogenic. Clinvar id is 143641.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MECP2	NM_001110792.2	c.658C>T	p.Gln220*	stop_gained	Exon 3 of 3	ENST00000453960.7	NP_001104262.1
MECP2	NM_004992.4	c.622C>T	p.Gln208*	stop_gained	Exon 4 of 4	ENST00000303391.11	NP_004983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MECP2	ENST00000453960.7	c.658C>T	p.Gln220*	stop_gained	Exon 3 of 3	1	NM_001110792.2	ENSP00000395535.2
MECP2	ENST00000303391.11	c.622C>T	p.Gln208*	stop_gained	Exon 4 of 4	1	NM_004992.4	ENSP00000301948.6

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 22

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rett syndrome Pathogenic:3

Sep 05, 2002

RettBASE

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

- -

Mar 18, 2024

Centre for Population Genomics, CPG

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as pathogenic. At least the following criteria are met: Predicted to result in loss of function, and LOF is a known mechanism of disease (PVS1). This variant is absent from gnomAD (PM2_Supporting). Has been observed in at least 2 individuals with phenotypes consistent with MECP2-related disease (PS4_Supporting). (PMID: 16225173, 16641581, 11269512) -

Jun 22, 2023

Neuberg Centre For Genomic Medicine, NCGM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The stop gained c.658C>T(p.Gln220Ter) variant in MECP2 gene has been reported previously in individual(s) affected with Rett syndrome (Vacca M, et al., 2001). The c.658C>T variant is absent in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic. Computational evidence (MutationTaster - Disease causing) predicts damaging effect on protein structure and function for this variant. The nucleotide change c.658C>T in MECP2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:2

Apr 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MECP2: PS2, PVS1:Strong, PM2, PS4:Supporting -

Aug 27, 2018

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Q208X variant in the MECP2 gene has been reported previously as de novo in an individual with Rett syndrome (Vacca et al., 2001). This variant is predicted to cause loss of normal protein function through protein truncation, as the last 279 amino acids are lost. The Q208X variant is not observed in large population cohorts (Lek et al., 2016). We interpret Q208X as a pathogenic variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.73	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	38
DANN	Uncertain	1.0
FATHMM_MKL	Pathogenic	0.98	D
PhyloP100		5.6
Vest4		0.92
GERP RS		5.5
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs61749729; hg19: chrX-153296657;