rs1557135461

Positions:

• chrX-154030638-TCGGAGCTCTCGGGCTCAGGTGGAGGTGGGGGCAGGGGTGGGAGCAGTGGCACGGGGGCCTTTGGGGACTCTGAGTGGTGGTGATGGTGGTGGTGCTCCTTCTTGGGGGGTGAGGAGGCGCTGCTGCTGCGCCCCTTGGGGCTGCTCTCCTTGCTTTTCCGCCCAGGGCTCTTACAGGTCTTCAGTCCTTTCCCGCTCTTCTCACCGAGGGTGGACACCAGCAGGGGCTTCACCACTTCCTTGACCTCGATGCTGACCGTCTCCCGGGTCTTGCGCTTCTTGATGGGGAGTACGGTCTCCTGCACAGATCGGATAGAAGACTCCTTCACGGCTTTCTTTTTGGCCTCGGCGGCAGCGGCTGCCACCACACTCCCCGGCTTTCGGCCCCGTTTCTTGGGAATGGCCTGAGGGTCGGCCTCAGCTTTTCGCTTCCTGCCGGGGCGTTTGATCACCATGACCTGGGTGGATGTGGTGGCCCCACCCCCCTCAGCCTTGCCCCCTGGCGAAGTTTGAAAAGGCATCTTGACAAGGAGCTTCCCAGGACTTTTCTCCAGGACCCTTTTCACCTGCACACCCTCTGACGTGGCCGCCTTGGGTCTCGTGGTGCCGCTCCCTTTGGGGCGTCCCCGGCCTCTGCCAGTTCCTGGAGCTTTGGGAGATTTGGGCTTCTTAGGTGGTTTCTGCTCTCGCCGGGAGGGGCTCC-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM4 PP5_Moderate

The NM_001386137.1(MECP2):​c.-128-54_520del​(p.Met1_Glu174del) variant causes a start lost, conservative inframe deletion, splice region change. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 16)
• Consequence: MECP2 NM_001386137.1 start_lost, conservative_inframe_deletion, splice_region
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• 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]

MECP2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001386137.1.
• PP5: Variant X-154030638-TCGGAGCTCTCGGGCTCAGGTGGAGGTGGGGGCAGGGGTGGGAGCAGTGGCACGGGGGCCTTTGGGGACTCTGAGTGGTGGTGATGGTGGTGGTGCTCCTTCTTGGGGGGTGAGGAGGCGCTGCTGCTGCGCCCCTTGGGGCTGCTCTCCTTGCTTTTCCGCCCAGGGCTCTTACAGGTCTTCAGTCCTTTCCCGCTCTTCTCACCGAGGGTGGACACCAGCAGGGGCTTCACCACTTCCTTGACCTCGATGCTGACCGTCTCCCGGGTCTTGCGCTTCTTGATGGGGAGTACGGTCTCCTGCACAGATCGGATAGAAGACTCCTTCACGGCTTTCTTTTTGGCCTCGGCGGCAGCGGCTGCCACCACACTCCCCGGCTTTCGGCCCCGTTTCTTGGGAATGGCCTGAGGGTCGGCCTCAGCTTTTCGCTTCCTGCCGGGGCGTTTGATCACCATGACCTGGGTGGATGTGGTGGCCCCACCCCCCTCAGCCTTGCCCCCTGGCGAAGTTTGAAAAGGCATCTTGACAAGGAGCTTCCCAGGACTTTTCTCCAGGACCCTTTTCACCTGCACACCCTCTGACGTGGCCGCCTTGGGTCTCGTGGTGCCGCTCCCTTTGGGGCGTCCCCGGCCTCTGCCAGTTCCTGGAGCTTTGGGAGATTTGGGCTTCTTAGGTGGTTTCTGCTCTCGCCGGGAGGGGCTCC-T is Pathogenic according to our data. Variant chrX-154030638-TCGGAGCTCTCGGGCTCAGGTGGAGGTGGGGGCAGGGGTGGGAGCAGTGGCACGGGGGCCTTTGGGGACTCTGAGTGGTGGTGATGGTGGTGGTGCTCCTTCTTGGGGGGTGAGGAGGCGCTGCTGCTGCGCCCCTTGGGGCTGCTCTCCTTGCTTTTCCGCCCAGGGCTCTTACAGGTCTTCAGTCCTTTCCCGCTCTTCTCACCGAGGGTGGACACCAGCAGGGGCTTCACCACTTCCTTGACCTCGATGCTGACCGTCTCCCGGGTCTTGCGCTTCTTGATGGGGAGTACGGTCTCCTGCACAGATCGGATAGAAGACTCCTTCACGGCTTTCTTTTTGGCCTCGGCGGCAGCGGCTGCCACCACACTCCCCGGCTTTCGGCCCCGTTTCTTGGGAATGGCCTGAGGGTCGGCCTCAGCTTTTCGCTTCCTGCCGGGGCGTTTGATCACCATGACCTGGGTGGATGTGGTGGCCCCACCCCCCTCAGCCTTGCCCCCTGGCGAAGTTTGAAAAGGCATCTTGACAAGGAGCTTCCCAGGACTTTTCTCCAGGACCCTTTTCACCTGCACACCCTCTGACGTGGCCGCCTTGGGTCTCGTGGTGCCGCTCCCTTTGGGGCGTCCCCGGCCTCTGCCAGTTCCTGGAGCTTTGGGAGATTTGGGCTTCTTAGGTGGTTTCTGCTCTCGCCGGGAGGGGCTCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 189711.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MECP2	NM_001110792.2	c.524_1225del	p.Gly175_Ser408del	disruptive_inframe_deletion	3/3	ENST00000453960.7	NP_001104262.1
MECP2	NM_004992.4	c.488_1189del	p.Gly163_Ser396del	disruptive_inframe_deletion	4/4	ENST00000303391.11	NP_004983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MECP2	ENST00000453960.7	c.524_1225del	p.Gly175_Ser408del	disruptive_inframe_deletion	3/3	1	NM_001110792.2	ENSP00000395535.2
MECP2	ENST00000303391.11	c.488_1189del	p.Gly163_Ser396del	disruptive_inframe_deletion	4/4	1	NM_004992.4	ENSP00000301948.6

Frequencies

GnomAD3 genomes Cov.: 16

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 16

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Rett syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	curation	Centre for Population Genomics, CPG	Jan 16, 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 removes >20% of the protein, including the transcriptional repression domain (TRD) of MECP2. Predicted to result in loss of function, and LOF is a known mechanism of disease (PVS1). Protein length changes due to in-frame deletions/insertions in a non-repeat region (PM4). This variant is absent from gnomAD (PM2_Supporting). -
Pathogenic, no assertion criteria provided	curation	RettBASE	Jan 21, 2008	- -

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: rs1557135461; hg19: chrX-153296089;