NM_001110792.2(MECP2):c.-7_62del (p.Met1_Leu21del) AND Rett syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 21, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003991404.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.-7_62del (p.Met1_Leu21del)]

NM_001110792.2(MECP2):c.-7_62del (p.Met1_Leu21del)

Genes:

LOC130068854:ATAC-STARR-seq lymphoblastoid silent region 21085 [Gene]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001110792.2(MECP2):c.-7_62del (p.Met1_Leu21del)

Other names:

NM_004992.4:c.-167_-99del

HGVS:

NC_000023.11:g.154097605_154097673del
NG_007107.3:g.44432_44500del
NG_162063.2:g.423_475del
NG_203268.1:g.63_131del
NM_001110792.2:c.-7_62delMANE SELECT
NM_001316337.2:c.-614_-546del
NM_001369391.2:c.-909_-841del
NM_001369392.2:c.-558_-490del
NM_001369393.2:c.-435_-367del69
NM_001386137.1:c.-839_-771del
NM_001386138.1:c.-727_-659del
NM_001386139.1:c.-603_-535del
NM_004992.4:c.-167_-99del
NP_001104262.1:p.Met1_Leu21del
LRG_764t1:c.-7_62del
LRG_764t2:c.-167_-99del
LRG_764:g.44432_44500del
LRG_764p1:p.Met1_Leu21del
NC_000023.10:g.153363062_153363130del

Molecular consequence:

NM_001316337.2:c.-614_-546del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369391.2:c.-909_-841del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369392.2:c.-558_-490del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369393.2:c.-435_-367del69 - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386137.1:c.-839_-771del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386138.1:c.-727_-659del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386139.1:c.-603_-535del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_004992.4:c.-167_-99del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001110792.2:c.-7_62del - inframe deletion - [Sequence Ontology: SO:0001822]
NM_001110792.2:c.-7_62del - initiator_codon_variant - [Sequence Ontology: SO:0001582]

Condition(s)

Name:: Rett syndrome (RTT)
Synonyms:: Autism, dementia, ataxia, and loss of purposeful hand use; Rett's disorder
Identifiers:: MONDO: MONDO:0010726; MedGen: C0035372; Orphanet: 3095; Orphanet: 778; OMIM: 312750

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zinc finger protein 135 [Centropristis striata]
zinc finger protein 135 [Centropristis striata]
gi|2572674157|ref|XP_059179927.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004808902	Centre for Population Genomics, CPG	criteria provided, single submitter (McKnight et al. (Hum Mutat. 2022))	Likely pathogenic (Feb 21, 2024)	germline	curation	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004808902

Centre for Population Genomics, CPG

criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))

Likely pathogenic
(Feb 21, 2024)

germline

curation

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Recommendations by the ClinGen Rett/Angelman-like expert panel for gene-specific variant interpretation methods.

McKnight D, Bean L, Karbassi I, Beattie K, Bienvenu T, Bonin H, Fang P, Chrisodoulou J, Friez M, Helgeson M, Krishnaraj R, Meng L, Mighion L, Neul J, Percy A, Ramsden S, Zoghbi H, Das S.

Hum Mutat. 2022 Aug;43(8):1097-1113. doi: 10.1002/humu.24302. Epub 2021 Dec 2.

PubMed [citation]

PMID:: 34837432
PMCID:: PMC9135956

Details of each submission

From Centre for Population Genomics, CPG, SCV004808902.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

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 likely pathogenic. At least the following criteria are met: Has been observed in at least 2 individuals with phenotypes consistent with MECP2-related disease (PS4_Supporting).PMID: 23810759, PMID: 16829352 This variant has been identified as a de novo occurrence in an individual with Rett syndrome without confirmation of paternity and maternity (PM6). PMID: 23810759 At least one individual with this variant has been reported with a clinical phenotype consistent with Rett syndrome (PP4). PMID: 16829352 This variant is absent from gnomAD (PM2_Supporting).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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