chrX:154031355:G>A Detail (hg38) (MECP2)

Information

Genome

Assembly Position
hg19 chrX:153,296,806-153,296,806 View the variant detail on this assembly version.
hg38 chrX:154,031,355-154,031,355

HGVS

Type Transcript Protein
RefSeq NM_001110792.1:c.509C>T NP_001104262.1:p.Thr170Met
NM_004992.3:c.473C>T NP_004983.1:p.Thr158Met
NM_001316337.1:c.432+41C>T
Summary

MGeND

Clinical significance Pathogenic Uncertain significance
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

[No Data.]

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 300005 OMIM
HGNC 6990 HGNC
Ensembl ENSG00000169057 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar
COSMIC COSM3033684 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Pathogenic other germline MGS000073
(TMGS000167) 		Kenjiro Kosaki
 Keio University
IRUD
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2024-02-28 criteria provided, multiple submitters, no conflicts Rett syndrome de novo germline inherited maternal unknown Detail
Pathogenic 2023-10-14 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2014-02-26 no assertion criteria provided Autism, susceptibility to, X-linked 3 unknown Detail
Pathogenic 2014-02-26 no assertion criteria provided Angelman syndrome unknown Detail
Pathogenic 2024-01-15 criteria provided, single submitter Severe neonatal-onset encephalopathy with microcephaly unknown germline maternal Detail
Pathogenic 2020-10-07 criteria provided, single submitter Inborn genetic diseases germline Detail
Pathogenic 2021-03-30 criteria provided, multiple submitters, no conflicts Severe neonatal-onset encephalopathy with microcephaly,syndromic X-linked intellectual disability Lubs type,Autism, susceptibility to, X-linked 3,Rett syndrome,X-linked intellectual disability-psychosis-macroorchidism syndrome germline unknown Detail
Pathogenic 2021-03-30 criteria provided, multiple submitters, no conflicts Severe neonatal-onset encephalopathy with microcephaly,syndromic X-linked intellectual disability Lubs type,Autism, susceptibility to, X-linked 3,Rett syndrome,X-linked intellectual disability-psychosis-macroorchidism syndrome germline unknown Detail
Pathogenic 2021-03-30 criteria provided, multiple submitters, no conflicts Severe neonatal-onset encephalopathy with microcephaly,syndromic X-linked intellectual disability Lubs type,Autism, susceptibility to, X-linked 3,Rett syndrome,X-linked intellectual disability-psychosis-macroorchidism syndrome germline unknown Detail
Pathogenic 2021-03-30 criteria provided, multiple submitters, no conflicts Severe neonatal-onset encephalopathy with microcephaly,syndromic X-linked intellectual disability Lubs type,Autism, susceptibility to, X-linked 3,Rett syndrome,X-linked intellectual disability-psychosis-macroorchidism syndrome germline unknown Detail
Pathogenic 2021-03-30 criteria provided, multiple submitters, no conflicts Severe neonatal-onset encephalopathy with microcephaly,syndromic X-linked intellectual disability Lubs type,Autism, susceptibility to, X-linked 3,Rett syndrome,X-linked intellectual disability-psychosis-macroorchidism syndrome germline unknown Detail
Pathogenic 2021-07-10 criteria provided, single submitter germline Detail
Pathogenic 2022-05-04 criteria provided, single submitter X-linked intellectual disability-psychosis-macroorchidism syndrome germline Detail
Pathogenic criteria provided, single submitter de novo Detail
Pathogenic 2024-03-14 criteria provided, single submitter syndromic X-linked intellectual disability Lubs type germline Detail
Pathogenic 2021-12-21 criteria provided, single submitter MECP2-related disorder unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 AUTISM, X-LINKED, SUSCEPTIBILITY TO, 3 (finding) NA CLINVAR Detail
0.360 ENCEPHALOPATHY, NEONATAL SEVERE, DUE TO MECP2 MUTATIONS NA CLINVAR Detail
0.247 Angelman syndrome NA CLINVAR Detail
0.800 Rett syndrome NA CLINVAR Detail
0.800 Rett syndrome Here, we have shown that frequent RTT-causing missense mutations (R106W, R133C, ... BeFree 18499664 Detail
0.800 Rett syndrome Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-bind... UNIPROT 10508514 Detail
0.800 Rett syndrome In classic RTT, poor growth was associated with worse development, higher diseas... BeFree 23035069 Detail
0.014 epilepsy MECP2 mutations most frequently associated with epilepsy were T158M (74%) and R1... BeFree 20231667 Detail
0.800 Rett syndrome Correlation between clinical severity in patients with Rett syndrome with a p.R1... BeFree 16905679 Detail
0.157 autistic disorder Females with the p.R306C or p.T158M mutations in the MECP2 gene were more likely... BeFree 17684768 Detail
0.005 Encephalopathies Sporadic case of fatal encephalopathy with neonatal onset associated with a T158... BeFree 12719401 Detail
0.005 Encephalopathies The phenotypes show a strong resemblance, and might in fact represent a clinical... BeFree 17236109 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Rett syndrome ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND not provided ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Autism, susceptibility to, X-linked 3 ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Angelman syndrome ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Severe neonatal-onset encephalopathy with microceph... ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Inborn genetic diseases ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Abnormality of the nervous system ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND X-linked intellectual disability-psychosis-macroorc... ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Neurodevelopmental delay ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND Syndromic X-linked intellectual disability Lubs typ... ClinVar Detail
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) AND MECP2-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
Here, we have shown that frequent RTT-causing missense mutations (R106W, R133C, F155S, T158M) locate... DisGeNET Detail
Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. DisGeNET Detail
In classic RTT, poor growth was associated with worse development, higher disease severity, and cert... DisGeNET Detail
MECP2 mutations most frequently associated with epilepsy were T158M (74%) and R106W (78%), and less ... DisGeNET Detail
Correlation between clinical severity in patients with Rett syndrome with a p.R168X or p.T158M MECP2... DisGeNET Detail
Females with the p.R306C or p.T158M mutations in the MECP2 gene were more likely to have an initial ... DisGeNET Detail
Sporadic case of fatal encephalopathy with neonatal onset associated with a T158M missense mutation ... DisGeNET Detail
The phenotypes show a strong resemblance, and might in fact represent a clinical-genetic entity of t... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs28934906 dbSNP
Genome
hg38
Position
chrX:154,031,355-154,031,355
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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