X-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C

Position:

• chrX-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

The NM_001110792.2(MECP2):​c.1199_1224del​(p.Pro400ArgfsTer8) variant causes a frameshift change. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P400P) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 16)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: MECP2 NM_001110792.2 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 5.66

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 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 47 pathogenic variants in the truncated region.
• PP5: Variant X-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C is Pathogenic according to our data. Variant chrX-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C is described in ClinVar as [Pathogenic]. Clinvar id is 143401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C is described in Lovd as [Pathogenic]. Variant chrX-154030639-CGGAGCTCTCGGGCTCAGGTGGAGGTG-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MECP2	NM_001110792.2	c.1199_1224del	p.Pro400ArgfsTer8	frameshift_variant	3/3	ENST00000453960.7
MECP2	NM_004992.4	c.1163_1188del	p.Pro388ArgfsTer8	frameshift_variant	4/4	ENST00000303391.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MECP2	ENST00000303391.11	c.1163_1188del	p.Pro388ArgfsTer8	frameshift_variant	4/4	1	NM_004992.4	P1
MECP2	ENST00000453960.7	c.1199_1224del	p.Pro400ArgfsTer8	frameshift_variant	3/3	1	NM_001110792.2
MECP2	ENST00000407218.5	c.*535_*560del		3_prime_UTR_variant	4/4	5
MECP2	ENST00000628176.2	c.*535_*560del		3_prime_UTR_variant	5/5	3

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 981331 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 311627

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 16

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rett syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Pathogenic, no assertion criteria provided	curation	RettBASE	Feb 15, 2011	- -
Pathogenic, criteria provided, single submitter	curation	Centre for Population Genomics, CPG	Aug 14, 2023	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 2.0, 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). Has been observed in at least 5 individuals with phenotypes consistent with MECP2-related disease (PS4). This variant is absent from gnomAD (PM2_Supporting). -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 22, 2016

The c.1163_1188del26 pathogenic mutation, located in coding exon 3 of the MECP2 gene, results from a deletion of 26 nucleotides between positions 1163 and 1188, causing a translational frameshift with a predicted alternate stop codon (p.P388Rfs*8). This pathogenic mutation has been reported in several individuals with Rett syndrome (Bienvenu T et al. Hum Mol Genet. 2000;9(9):1377-84; Philippe C et al. Eur J Med Genet;49:9-18). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267608600; hg19: chrX-153296090;