NM_001110792.2(MECP2):c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT (p.Pro401_Pro417delinsTer) AND Rett syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 23, 2023
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:: RCV003153040.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT (p.Pro401_Pro417delinsTer)]

NM_001110792.2(MECP2):c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT (p.Pro401_Pro417delinsTer)

Gene:

MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001110792.2(MECP2):c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT (p.Pro401_Pro417delinsTer)

HGVS:

NC_000023.11:g.154030615_154030664delinsACTCTGAGTGGTGGTGATGGTGGTGGTGCTCCTTCTTGGGGGGTGCTCAG
NG_007107.3:g.111440_111489delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001110792.2:c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGTMANE SELECT
NM_001316337.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001369391.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001369392.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001369393.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001369394.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001386137.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001386138.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_001386139.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NM_004992.4:c.1164_1213delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
NP_001104262.1:p.Pro401_Pro417delinsTer
NP_001303266.1:p.Pro296_Pro312delinsTer
NP_001356320.1:p.Pro296_Pro312delinsTer
NP_001356321.1:p.Pro296_Pro312delinsTer
NP_001356322.1:p.Pro296_Pro312delinsTer
NP_001356323.1:p.Pro296_Pro312delinsTer
NP_001373066.1:p.Pro166_Pro182delinsTer
NP_001373067.1:p.Pro166_Pro182delinsTer
NP_001373068.1:p.Pro166_Pro182delinsTer
NP_004983.1:p.Pro389_Pro405delinsTer
LRG_764t1:c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
LRG_764t2:c.1164_1213delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
LRG_764:g.111440_111489delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT
LRG_764p1:p.Pro401_Pro417delinsTer
LRG_764p2:p.Pro389_Pro405delinsTer
NC_000023.10:g.153296066_153296115delinsACTCTGAGTGGTGGTGATGGTGGTGGTGCTCCTTCTTGGGGGGTGCTCAG

Molecular consequence:

NM_001110792.2:c.1200_1249delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001316337.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001369391.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001369392.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001369393.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001369394.2:c.885_934delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001386137.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001386138.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_001386139.1:c.495_544delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]
NM_004992.4:c.1164_1213delinsCTGAGCACCCCCCAAGAAGGAGCACCACCACCATCACCACCACTCAGAGT - nonsense - [Sequence Ontology: SO:0001587]

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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Homo sapiens RUN domain containing 3A (RUNDC3A), transcript variant 1, mRNA
gi|1519313797|ref|NM_001144825.2|

Nucleotide
Deafness-Dystonia-Optic Neuronopathy Syndrome - GeneReviews®
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Hereditary sensory and autonomic neuropathy type 6
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003841751	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003841751

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 23, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV003841751.1

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Mar 26, 2023

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