chrX-154030661-AGGTGGGG-A

Position:

chrX-154030661-AGGTGGGG-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 16P and 4B. PVS1PP5_Very_StrongBS2

The NM_001110792.2(MECP2):c.1196_1202del(p.Pro399LeufsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000399 in 552,051 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P399P) has been classified as Benign.

Frequency

Genomes: 𝑓 0.000061 ( 0 hom., 0 hem., cov: 0)

Exomes 𝑓: 0.000039 ( 0 hom. 4 hem. )

Consequence

MECP2
NM_001110792.2 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:4

Conservation

PhyloP100: 3.20

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 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 50 pathogenic variants in the truncated region.

PP5

Variant X-154030661-AGGTGGGG-A is Pathogenic according to our data. Variant chrX-154030661-AGGTGGGG-A is described in ClinVar as [Pathogenic]. Clinvar id is 143384.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154030661-AGGTGGGG-A is described in Lovd as [Pathogenic].

BS2

High Hemizygotes in GnomAdExome4 at 4 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MECP2	NM_001110792.2 linkuse as main transcript	c.1196_1202del	p.Pro399LeufsTer20	frameshift_variant	3/3	ENST00000453960.7
MECP2	NM_004992.4 linkuse as main transcript	c.1160_1166del	p.Pro387LeufsTer20	frameshift_variant	4/4	ENST00000303391.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MECP2	ENST00000303391.11 linkuse as main transcript	c.1160_1166del	p.Pro387LeufsTer20	frameshift_variant	4/4	1	NM_004992.4	P1	P51608-1
MECP2	ENST00000453960.7 linkuse as main transcript	c.1196_1202del	p.Pro399LeufsTer20	frameshift_variant	3/3	1	NM_001110792.2		P51608-2
MECP2	ENST00000407218.5 linkuse as main transcript	c.532_538del		3_prime_UTR_variant	4/4	5
MECP2	ENST00000628176.2 linkuse as main transcript	c.532_538del		3_prime_UTR_variant	5/5	3

Frequencies

GnomAD3 genomes

AF:

0.0000609

AC:

AN:

16414

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

4652

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000115

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000755

AC:

AN:

132529

Hom.:

AF XY:

0.0000204

AC XY:

AN XY:

49033

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000155

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000392

AC:

AN:

535637

Hom.:

AF XY:

0.0000255

AC XY:

AN XY:

156659

show subpopulations

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:

0.0000462

Gnomad4 OTH exome

AF:

0.0000528

GnomAD4 genome

AF:

0.0000609

AC:

AN:

16414

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

4652

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000115

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Rett syndrome

Pathogenic:3

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). This variant is absent from the NHLBI exome sequencing project (PM2_Supporting). It has been observed in at least 3 individuals with phenotypes consistent with MECP2-related disease (PS4_Moderate, RettBase internal database, PMID: 20031356, PMID: 21160487, PMID: 15389714). -
Pathogenic, no assertion criteria provided	curation	RettBASE	Nov 01, 2011	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Feb 14, 2023	The frameshift c.1196_1202del(p.Pro399LeufsTer20) variant in MECP2 gene has been reported previously in individual(s) affected with Rett syndrome (Hadzsiev K, et. al., 2011; Kárteszi J, et. al., 2004). The p.Pro399LeufsTer20 variant has been reported with allele frequency of 0.0008% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. This variant causes a frameshift starting with codon Proline 399, changes this amino acid to Leucine residue, and creates a premature Stop codon at position 20 of the new reading frame, denoted p.Pro399LeufsTer20. 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:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 14, 2016

The c.1160_1166delCCCCACC pathogenic variant in the MECP2 gene has been reported previously in association with Rett syndrome (Hadzsiev et al., 2011; Karteszi et al., 2004; Monnerat et al., 2010). The deletion causes a frameshift starting with codon Proline 387, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 20 of the new reading frame, denoted p.P387LfsX20. The c.1160_1166delCCCCACC variant is predicted to cause loss of normal protein function through protein truncation, as the last 100 amino acids are replaced with 19 incorrect ones. Additionally, this variant was not observed in approximately 6,300 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over