X-154031453-G-C

Position:

• chrX-154031453-G-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS4 PP3 PM6_Strong PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The c.378-3C>G variant in MECP2 has been observed in at least 5 individuals with Angelman syndrome (PMID:15737703, Rettbase, GeneDx internal data) (PS4). It has been reported in at least 2 unconfirmed de novo occurrences in individuals with Rett syndrome (PMID 15737703, 20142466) (PM6_strong). The c.378-3C>G variant in MECP2 is absent from gnomAD (PM2_supporting). Splice prediction analysis using multiple computational tools suggests an impact to splicing (PP3). In summary, the c.378-3C>G variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS4, PM6_strong, PM2_supporting, PP3). LINK:https://erepo.genome.network/evrepo/ui/classification/CA233152/MONDO:0010726/016

• Frequency: Genomes: not found (cov: 23)
• Consequence: MECP2 NM_001110792.2 splice_region, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic reviewed by expert panel P:16 O:1
• Conservation: PhyloP100: 4.72

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 10 ACMG points.

• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM6: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MECP2	NM_001110792.2	c.414-3C>G		splice_region_variant, intron_variant		ENST00000453960.7	NP_001104262.1
MECP2	NM_004992.4	c.378-3C>G		splice_region_variant, intron_variant		ENST00000303391.11	NP_004983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MECP2	ENST00000453960.7	c.414-3C>G		splice_region_variant, intron_variant		1	NM_001110792.2	ENSP00000395535.2
MECP2	ENST00000303391.11	c.378-3C>G		splice_region_variant, intron_variant		1	NM_004992.4	ENSP00000301948.6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:16 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Rett syndrome Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jan 28, 2021	- -
Pathogenic, no assertion criteria provided	curation	RettBASE	Feb 18, 2008	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Nov 30, 2018	PS2, PM2, PP4, PP5 -
Pathogenic, reviewed by expert panel	curation	ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel	Mar 26, 2021	The c.378-3C>G variant in MECP2 has been observed in at least 5 individuals with Angelman syndrome (PMID: 15737703, Rettbase, GeneDx internal data) (PS4). It has been reported in at least 2 unconfirmed de novo occurrences in individuals with Rett syndrome (PMID 15737703, 20142466) (PM6_strong). The c.378-3C>G variant in MECP2 is absent from gnomAD (PM2_supporting). Splice prediction analysis using multiple computational tools suggests an impact to splicing (PP3). In summary, the c.378-3C>G variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS4, PM6_strong, PM2_supporting, PP3). -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Intron variant. In silico tools predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 1.00). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 15737703). The variant has been previously reported as assumed (i.e. paternity and maternity not confirmed) de novo in at least one similarly affected unrelated individual (PMID: 15737703, 20142466). The variant has been reported multiple times as an established pathogenic variant (ClinVar ID: VCV000156068 / PMID: 15737703). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 20, 2023	Variant summary: MECP2 c.378-3C>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: three predict the variant abolishes the canonical 3' acceptor site, while four predict the variant creates a 3' acceptor site two nucleotides upstream from the original site, which is predicted to cause a frameshift, if utilized. Since the variant is located at the last intron-exon junction, it is not expected to cause nonsense mediated decay (NMD), but is predicted to cause a truncation of the encoded protein, removing a large part of the 486 amino acids long protein (and likely replacing it with an incorrect sequence). However, these predictions have yet to be confirmed by functional studies. The variant was absent in 181290 control chromosomes (gnomAD). The variant, c.378-3C>G, has been reported in the literature in at least two affected individuals as a de novo occurrence, i.e. in one female with classical Rett syndrome (Fukuda_2005), and in one male in who had acquired (progressive) microcephaly, regression of milestones, mitochondrial dysfunction, and episodic rigidity (Condie_2010). In addition, the variant was also reported in another male affected with progressive encephalopathy (Neul_2019) and multiple females diagnosed with classical (or unspecified) Rett syndrome (e.g. Bisgaard_2015, Liu_2022, RettBase (PMID: 28544139)). These data indicate that the variant likely associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 20142466, 15737703, 24508304, 30536762, 26254891, 26228846, 34619114). Ten other submitters, including an expert panel (ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel), have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic (n=5; including the expert panel) / likely pathogenic (n=5). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Centre for Population Genomics, CPG	Jan 10, 2024	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: This variant has been identified as a de novo occurrence in at least 2 individuals with Rett syndrome, without confirmation of paternity and maternity (PM6_Strong). Has been observed in at least 5 individuals with phenotypes consistent with MECP2-related disease (PS4).(PMID: 15737703, Variation ID:156068). This variant is absent from gnomAD (PM2_Supporting). -

not provided Pathogenic:3 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 28, 2022	PP3, PP5, PM2, PM6_strong, PS4_moderate -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 19, 2024	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 26254891, 25525159, 15737703, 20142466, 24508304, 30536762, 34619114) -
not provided, flagged submission	literature only	RettBASE	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 16, 2018	- -

Severe neonatal-onset encephalopathy with microcephaly Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 30, 2023

This sequence change falls in intron 3 of the MECP2 gene. It does not directly change the encoded amino acid sequence of the MECP2 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of Rett syndrome (PMID: 15737703, 24508304, 30536762). In at least one individual the variant was observed to be de novo. This variant is also known as Ex4 acceptor site. ClinVar contains an entry for this variant (Variation ID: 156068). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Oct 03, 2018

The MECP2 c.378-3C>G variant (rs267608465), is reported in the literature in multiple females affected with classic Rett syndrome (Fukuda 2005, Kalman 2014), and also in a male affected with Rett syndrome (Condie 2010). This variant is reported as pathogenic in ClinVar (Variation ID: 156068), and is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. This variant abolishes the canonical splice acceptor site of intron 3, which is likely to disrupt gene function by creating a novel spice acceptor site that is predicted to cause a frameshift. Based on available information, the c.378-3C>G variant is considered to be pathogenic. References: Condie J et al. Acquired microcephaly, regression of milestones, mitochondrial dysfunction, and episodic rigidity in a 46,XY male with a de novo MECP2 gene mutation. J Child Neurol. 2010 May;25(5):633-6. Fukuda T et al. Methyl-CpG binding protein 2 gene (MECP2) variations in Japanese patients with Rett syndrome: pathological mutations and polymorphisms. Brain Dev. 2005 Apr;27(3):211-7. Kalman LV et al. Development of a genomic DNA reference material panel for Rett syndrome (MECP2-related disorders) genetic testing. J Mol Diagn. 2014 Mar;16(2):273-9. -

Syndromic X-linked intellectual disability Lubs type Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 25, 2024

- -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 03, 2023

The c.378-3C>G intronic alteration results from a C to G substitution 3 nucleotides before coding exon 3 of the MECP2 gene. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been detected twice as de novo occurrences: once in a female with a diagnosis of typical Rett syndrome (Fukuda, 2005) and once in a male with acquired microcephaly, increased muscle tone and reflexes, mitochondrial impairments, and regression (Condie, 2010). It was also identified in a male with progressive encephalopathy (Neul, 2019). Additionally, this alteration was detected in two individuals diagnosed with Rett syndrome; however, no specific phenotypic information was provided (Kalman, 2014; Krishnaraj, 2017). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as likely pathogenic. -

Rett syndrome;C0796222:X-linked intellectual disability-psychosis-macroorchidism syndrome;C1845336:Autism, susceptibility to, X-linked 3;C1846058:Syndromic X-linked intellectual disability Lubs type;C1968556:Severe neonatal-onset encephalopathy with microcephaly Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Mar 30, 2021

MECP2 NM_004992.3 exon 4 c.378-3C>G p.?: This variant has been reported in the literature as de novo in one female with classic Rett syndrome, as well as in the RettBASE in two additional females with classic Rett syndrome (Fukuda 2005 PMID:15737703, Christodoulou 2003 PMID:12673788). This variant is not present in large control databases, and it is present in ClinVar (Variation ID:156068). Computational tools designed to predict splicing suggest an effect from this variant through creation of a new acceptor site. However, further studies are needed to understand its impact. Of note, the vast majority of pathogenic variants are identified in exon 4 of this gene, which encodes for the methyl binding domain and transcription repression domain; this intronic variant falls just outside of that region (Philippe 2006 PMID:16473305). In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as likely pathogenic. -

MECP2-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 27, 2024

The MECP2 c.378-3C>G variant is predicted to interfere with splicing. This variant has been reported in individuals with MECP2-related disorders (see, for example, Fukuda et al. 2005. PubMed ID: 15737703; Bisgaard et al. 2015. PubMed ID: 26228846; Neul et al. 2019. PubMed ID: 30536762). It has been reported to occur de novo (Fukuda et al. 2005. PubMed ID: 15737703; Condie et al. 2010. PubMed ID: 20142466). This variant is predicted to alter splicing based on available splicing prediction programs (SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751). However, the use of computer prediction programs is not equivalent to functional evidence. This variant has not been reported in a large population database, indicating itt is rare. This variant is interpreted as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Uncertain	25
DANN	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		1.0		Position offset: -1
DS_AL_spliceai		0.99		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs267608465; hg19: chrX-153296904;