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 to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0 , this variant is classified as Benign . At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 2.0 (BA1).
ClinVar Genomic variation as it relates to human health
NM_001110792.2(MECP2):c.414-17del
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(13)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Benign/Likely benign
13
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001110792.2(MECP2):c.414-17del
Variation ID: 156063 Accession: VCV000156063.20
- Type and length
-
Deletion, 1 bp
- Location
-
Cytogenetic: Xq28 X: 154031467 (GRCh38) [ NCBI UCSC ] X: 153296918 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Sep 26, 2014 May 1, 2024 Jan 31, 2024 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001110792.2:c.414-17del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_004992.4:c.378-17del MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001316337.2:c.99-17del intron variant NM_001369391.2:c.99-17del intron variant NM_001369392.2:c.99-17del intron variant NM_001369393.2:c.99-17del intron variant NM_001369394.2:c.99-17del intron variant NM_001386137.1:c.-183-17del intron variant NM_001386138.1:c.-183-17del intron variant NM_001386139.1:c.-183-17del intron variant NM_004992.3:c.378-17delT NC_000023.11:g.154031469del NC_000023.10:g.153296920del NG_007107.3:g.110637del LRG_764:g.110637del LRG_764t1:c.414-17del LRG_764t2:c.378-17del AJ132917.1:c.378-17delT - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000023.11:154031466:AAA:AA
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
-
0.00132 (AA)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| MECP2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1902 | 2230 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Benign/Likely benign (6) |
criteria provided, multiple submitters, no conflicts
|
Jun 2, 2017 | RCV000144110.10 | |
| Benign (3) |
criteria provided, single submitter
|
Jul 20, 2015 | RCV000168682.9 | |
| Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Aug 14, 2023 | RCV000202549.3 | |
| Benign (1) |
criteria provided, single submitter
|
Sep 23, 2015 | RCV002362776.2 | |
| Benign (1) |
criteria provided, single submitter
|
Jan 31, 2024 | RCV002055862.6 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Benign
(Jun 01, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Rett syndrome
Affected status: yes
Allele origin:
germline
|
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital
Accession: SCV000257509.2
First in ClinVar: Dec 18, 2015 Last updated: Jun 03, 2019 |
Sex: female
|
|
|
Benign
(Jan 31, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Severe neonatal-onset encephalopathy with microcephaly
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002432132.3
First in ClinVar: Apr 08, 2022 Last updated: Feb 14, 2024 |
|
|
|
Benign
(Jul 20, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000330972.4
First in ClinVar: Dec 06, 2016 Last updated: May 03, 2018 |
Number of individuals with the variant: 3
Sex: mixed
|
|
|
Benign
(Aug 14, 2023)
|
criteria provided, single submitter
Method: curation
|
Rett syndrome
(X-linked inheritance)
Affected status: unknown
Allele origin:
germline
|
Centre for Population Genomics, CPG
Accession: SCV004098860.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
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 … (more)
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 to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0 , this variant is classified as Benign . At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 2.0 (BA1). (less)
|
|
|
Benign
(Sep 23, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV002625773.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
|
|
Likely benign
(Jun 02, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: not provided
Allele origin:
germline
|
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000609828.1
First in ClinVar: Sep 26, 2014 Last updated: Sep 26, 2014 |
|
|
|
Benign
(Mar 03, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001870203.1
First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
|
|
|
Benign
(Mar 23, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004220013.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
|
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742659.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001970903.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
|
|
|
Benign
(Dec 05, 2013)
|
no assertion criteria provided
Method: curation
|
Not specified
Affected status: not provided
Allele origin:
unknown,
paternal,
germline,
maternal
|
RettBASE
Accession: SCV000222412.1
First in ClinVar: Apr 22, 2015 Last updated: Apr 22, 2015 |
Observation 1:
Number of individuals with the variant: 1
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - normal control
Observation 2:
Number of individuals with the variant: 1
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - unaffected family member
Observation 3:
Number of individuals with the variant: 1
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 4:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 5:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 6:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 7:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 8:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 9:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 10:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 11:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 12:
Number of individuals with the variant: 1
Family history: No
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 13:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 14:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 15:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 16:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 17:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 18:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 19:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: not stated
Comment on evidence:
Rett syndrome - not certain
Observation 20:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - sporadic mental retardation
Observation 21:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - sporadic mental retardation
Observation 22:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 23:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 24:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 25:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 26:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 27:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 28:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 29:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 30:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - non-specfic mental retardation
Observation 31:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - sporadic mental retardation
Observation 32:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 33:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 34:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 35:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 36:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 37:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 38:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 39:
Number of individuals with the variant: 1
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - unaffected family member
Observation 40:
Number of individuals with the variant: 1
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 41:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 42:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 43:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 44:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 45:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 46:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 47:
Number of individuals with the variant: 1
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 48:
Number of individuals with the variant: 1
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 49:
Number of individuals with the variant: 1
Sex: female
Tissue: Blood
Comment on evidence:
Not known
Observation 50:
Number of individuals with the variant: 1
Sex: female
Tissue: Blood
Comment on evidence:
Not known
Observation 51:
Number of individuals with the variant: 1
Sex: female
Tissue: Not Known
Comment on evidence:
Not known
Observation 52:
Number of individuals with the variant: 1
Sex: female
Tissue: Not Known
Comment on evidence:
Not known
Observation 53:
Number of individuals with the variant: 1
Sex: male
Comment on evidence:
Not Rett synd. - Alcoholism
Observation 54:
Number of individuals with the variant: 1
Tissue: blood
Comment on evidence:
Not Rett synd. - Autism
Observation 55:
Number of individuals with the variant: 1
Family history: Yes
Sex: male
Tissue: Blood
Comment on evidence:
Not Rett synd. - autism only
Observation 56:
Number of individuals with the variant: 1
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - mental retardation
Observation 57:
Number of individuals with the variant: 1
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - mental retardation
Observation 58:
Number of individuals with the variant: 1
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 59:
Number of individuals with the variant: 1
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 60:
Number of individuals with the variant: 1
Sex: female
Tissue: blood
Comment on evidence:
Not Rett synd. - non-Rett syndrome control
Observation 61:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 62:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 63:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 64:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 65:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 66:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 67:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 68:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 69:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 70:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 71:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 72:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 73:
Number of individuals with the variant: 1
Family history: No
Tissue: not stated
Comment on evidence:
Not Rett synd. - normal control
Observation 74:
Number of individuals with the variant: 1
Family history: Yes
Sex: male
Tissue: Blood
Comment on evidence:
Not Rett synd. - Not certain
Observation 75:
Number of individuals with the variant: 1
Family history: Yes
Sex: male
Tissue: Blood
Comment on evidence:
Not Rett synd. - Not certain
Observation 76:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Not known
Comment on evidence:
Not Rett synd. - Sporadic mental retardation
Observation 77:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Not known
Comment on evidence:
Not Rett synd. - Sporadic mental retardation
Observation 78:
Number of individuals with the variant: 1
Family history: No
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - Sporadic mental retardation
Observation 79:
Number of individuals with the variant: 1
Family history: No
Sex: male
Tissue: blood
Comment on evidence:
Not Rett synd. - Sporadic mental retardation
Observation 80:
Number of individuals with the variant: 1
Family history: No
Tissue: Blood
Comment on evidence:
Not Rett synd. - Unaffected family member
Observation 81:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Blood
Comment on evidence:
Not Rett synd. - Unaffected family member
Observation 82:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: blood
Comment on evidence:
Rett syndrome - Atypical
Observation 83:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: blood
Comment on evidence:
Rett syndrome - Classical
Observation 84:
Number of individuals with the variant: 1
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 85:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 86:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
Observation 87:
Number of individuals with the variant: 1
Family history: No
Sex: female
Tissue: Blood
Comment on evidence:
Rett syndrome - Not certain
|
|
|
Benign
(Apr 03, 2015)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Additional submitter:
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000804263.1
First in ClinVar: Sep 01, 2018 Last updated: Sep 01, 2018 |
|
|
|
not provided
(-)
|
Flagged submission
flagged submission
Method: not provided
Reason: This record appears to be redundant with a more recent record from the same submitter.
Notes: SCV000189186 appears to be redundant with SCV000222412.
(less)
Notes: SCV000189186 appears to
(...more)
Source: NCBI
|
not provided
Affected status: not provided
Allele origin:
not provided
|
RettBASE
Accession: SCV000189186.1
First in ClinVar: Sep 26, 2014 Last updated: Sep 26, 2014 |
|
|
| click to load more click to collapse | |||||
| Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more | |||||
Comment:
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Comment:
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 to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0 , this variant is classified as Benign . At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 2.0 (BA1).
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| MECP2 gene study in a large cohort: testing of 240 female patients and 861 healthy controls (519 females and 342 males). | Maortua H | The Journal of molecular diagnostics : JMD | 2013 | PMID: 23810759 |
| Identification and characterization of novel sequence variations in MECP2 gene in Rett syndrome patients. | Monnerat LS | Brain & development | 2010 | PMID: 20031356 |
| MECP2 coding sequence and 3'UTR variation in 172 unrelated autistic patients. | Coutinho AM | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 2007 | PMID: 17427193 |
| Mutation analysis of the MECP2 gene in patients of Slavic origin with Rett syndrome: novel mutations and polymorphisms. | Zahorakova D | Journal of human genetics | 2007 | PMID: 17387578 |
| Mutation screening of the MECP2 gene in a large cohort of 613 fragile-X negative patients with mental retardation. | Lesca G | European journal of medical genetics | 2007 | PMID: 17383248 |
| Screening for MECP2 mutations in Spanish patients with an unexplained mental retardation. | Tejada MI | Clinical genetics | 2006 | PMID: 16879196 |
| A new cohort of MECP2 mutation screening in unexplained mental retardation: careful re-evaluation is the best indicator for molecular diagnosis. | Donzel-Javouhey A | American journal of medical genetics. Part A | 2006 | PMID: 16763963 |
| MECP2 mutations are an infrequent cause of mental retardation associated with neurological problems in male patients. | Moog U | Brain & development | 2006 | PMID: 16376510 |
| MECP2 mutation analysis in patients with mental retardation. | Ylisaukko-Oja T | American journal of medical genetics. Part A | 2005 | PMID: 15578581 |
| MECP2 structural and 3'-UTR variants in schizophrenia, autism and other psychiatric diseases: a possible association with autism. | Shibayama A | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 2004 | PMID: 15211631 |
| Screening for mutations in the MECP2 (Rett syndrome) gene in Gilles de la Tourette syndrome. | Rosa AL | Archives of neurology | 2003 | PMID: 12707062 |
| Mutation analysis of the coding sequence of the MECP2 gene in infantile autism. | Beyer KS | Human genetics | 2002 | PMID: 12384770 |
| MECP2 mutation screening in Swedish classical Rett syndrome females. | Erlandson A | European child & adolescent psychiatry | 2001 | PMID: 11469283 |
| Mutation spectrum in patients with Rett syndrome in the German population: Evidence of hot spot regions. | Laccone F | Human mutation | 2001 | PMID: 11241840 |
| Mutations in the MECP2 gene in a cohort of girls with Rett syndrome. | Hampson K | Journal of medical genetics | 2000 | PMID: 10991689 |
| http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MECP2 | - | - | - | - |
| https://erepo.clinicalgenome.org/evrepo/ui/interpretation/ad04a888-8713-41d0-bbd5-7ddbf0a07339 | - | - | - | - |
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Text-mined citations for rs61753982 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.