chrX:153296119:G>A Detail (hg19) (MECP2)

Information

Genome

Assembly Position
hg19 chrX:153,296,119-153,296,119
hg38 chrX:154,030,668-154,030,668 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004992.3:c.1160C>T NP_004983.1:p.Pro387Leu
NM_001110792.1:c.1196C>T NP_001104262.1:p.Pro399Leu
NM_001316337.1:c.*532C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
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 tgv67029442 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2002-04-10 no assertion criteria provided X-linked intellectual disability-psychosis-macroorchidism syndrome maternal Detail
Likely benign 2021-04-13 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely benign 2017-11-22 criteria provided, single submitter not specified germline Detail
Benign 2023-11-30 criteria provided, single submitter Severe neonatal-onset encephalopathy with microcephaly germline Detail
Benign 2021-12-13 reviewed by expert panel Rett syndrome germline Detail
Uncertain significance 2016-10-10 criteria provided, single submitter Inborn genetic diseases germline Detail
Likely benign 2022-01-03 criteria provided, single submitter Rett syndrome,Autism, susceptibility to, X-linked 3,syndromic X-linked intellectual disability Lubs type,Severe neonatal-onset encephalopathy with microcephaly,X-linked intellectual disability-psychosis-macroorchidism syndrome unknown Detail
Likely benign 2022-01-03 criteria provided, single submitter Rett syndrome,Autism, susceptibility to, X-linked 3,syndromic X-linked intellectual disability Lubs type,Severe neonatal-onset encephalopathy with microcephaly,X-linked intellectual disability-psychosis-macroorchidism syndrome unknown Detail
Likely benign 2022-01-03 criteria provided, single submitter Rett syndrome,Autism, susceptibility to, X-linked 3,syndromic X-linked intellectual disability Lubs type,Severe neonatal-onset encephalopathy with microcephaly,X-linked intellectual disability-psychosis-macroorchidism syndrome unknown Detail
Likely benign 2022-01-03 criteria provided, single submitter Rett syndrome,Autism, susceptibility to, X-linked 3,syndromic X-linked intellectual disability Lubs type,Severe neonatal-onset encephalopathy with microcephaly,X-linked intellectual disability-psychosis-macroorchidism syndrome unknown Detail
Likely benign 2022-01-03 criteria provided, single submitter Rett syndrome,Autism, susceptibility to, X-linked 3,syndromic X-linked intellectual disability Lubs type,Severe neonatal-onset encephalopathy with microcephaly,X-linked intellectual disability-psychosis-macroorchidism syndrome unknown Detail
Likely benign 2022-04-08 criteria provided, single submitter MECP2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND X-linked intellectual disability-psychosis-macroor... ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND not provided ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND not specified ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND Severe neonatal-onset encephalopathy with microcep... ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND Rett syndrome ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND Inborn genetic diseases ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND multiple conditions ClinVar Detail
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu) AND MECP2-related disorder ClinVar 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
rs63390262 dbSNP
Genome
hg19
Position
chrX:153,296,119-153,296,119
Variant Type
snv
Reference Allele
G
Alternative Allele
A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.60to99.80
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs63390262
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12837
East Asian Chromosome Counts (ExAC)
6369
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
81142
Allele Counts in All Race (ExAC)
7
Heterozygous Counts in All Race (ExAC)
3
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.62685169209534E-5
East Asian Hemizygous Counts (ExAC)
0
Hemizygous Counts in All Race (ExAC)
4
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