NM_001110792.2(MECP2):c.411C>A (p.Ile137=) AND not specified

Germline classification:: Benign (7 submissions)
Last evaluated:: Jan 25, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000081201.30

Allele description [Variation Report for NM_001110792.2(MECP2):c.411C>A (p.Ile137=)]

NM_001110792.2(MECP2):c.411C>A (p.Ile137=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001110792.2(MECP2):c.411C>A (p.Ile137=)

Other names:

p.I125I:ATC>ATA; NM_001110792.2(MECP2):c.411C>A; p.Ile137=

HGVS:

NC_000023.11:g.154032209G>T
NG_007107.3:g.109895C>A
NM_001110792.2:c.411C>AMANE SELECT
NM_001316337.2:c.96C>A
NM_001369391.2:c.96C>A
NM_001369392.2:c.96C>A
NM_001369393.2:c.96C>A
NM_001369394.2:c.96C>A
NM_001386137.1:c.-186C>A
NM_001386138.1:c.-186C>A
NM_001386139.1:c.-186C>A
NM_004992.4:c.375C>A
NP_001104262.1:p.Ile137=
NP_001303266.1:p.Ile32=
NP_001356320.1:p.Ile32=
NP_001356321.1:p.Ile32=
NP_001356322.1:p.Ile32=
NP_001356323.1:p.Ile32=
NP_004983.1:p.Ile125=
NP_004983.1:p.Ile125=
LRG_764t1:c.411C>A
LRG_764t2:c.375C>A
AJ132917.1:c.375C>A
LRG_764:g.109895C>A
LRG_764p1:p.Ile137=
LRG_764p2:p.Ile125=
NC_000023.10:g.153297660G>T
NG_007107.2:g.109919C>A
NM_001110792.1:c.411C>A
NM_004992.3:c.375C>A
NP_004983.1:p.(=)

Links:

dbSNP: rs146107517

NCBI 1000 Genomes Browser:

rs146107517

Molecular consequence:

NM_001386137.1:c.-186C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386138.1:c.-186C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386139.1:c.-186C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001110792.2:c.411C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001316337.2:c.96C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369391.2:c.96C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369392.2:c.96C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369393.2:c.96C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369394.2:c.96C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004992.4:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Mus musculus SECIS binding protein 2, mRNA (cDNA clone IMAGE:1447063), partial c...
Mus musculus SECIS binding protein 2, mRNA (cDNA clone IMAGE:1447063), partial cds
gi|24433541|gb|BC038877.1|

Nucleotide
SLC35E3 [Gracilinanus agilis]
SLC35E3 [Gracilinanus agilis]
Gene ID:123249282

Gene
Pdw03_5920 [Penicillium digitatum]
Pdw03_5920 [Penicillium digitatum]
Gene ID:26229333

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000113109	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Sep 4, 2013)	germline	clinical testing	Citation Link,
SCV000170216	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 1, 2013)	germline	clinical testing	Citation Link,
SCV000188072	RettBASE	no assertion criteria provided	Benign (Nov 1, 2011)	unknown	curation	PubMed (4) [See all records that cite these PMIDs] 10767337, 11055898, 20479760, 21160487
SCV000247965	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Apr 16, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000257508	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	no assertion criteria provided	Benign (May 9, 2007)	germline	clinical testing
SCV000310760	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003800987	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jan 25, 2023)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	not provided	not provided	1	not provided	clinical testing
not provided	unknown	not provided	7	not provided	not provided	7	No	curation

Citations

PubMed

Long-read sequence analysis of the MECP2 gene in Rett syndrome patients: correlation of disease severity with mutation type and location.

Cheadle JP, Gill H, Fleming N, Maynard J, Kerr A, Leonard H, Krawczak M, Cooper DN, Lynch S, Thomas N, Hughes H, Hulten M, Ravine D, Sampson JR, Clarke A.

Hum Mol Genet. 2000 Apr 12;9(7):1119-29. Erratum in: Hum Mol Genet 2000 Jul 1;9(11):1717.

PubMed [citation]

PMID:: 10767337

Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms.

Buyse IM, Fang P, Hoon KT, Amir RE, Zoghbi HY, Roa BB.

Am J Hum Genet. 2000 Dec;67(6):1428-36. Epub 2000 Oct 30.

PubMed [citation]

PMID:: 11055898
PMCID:: PMC1287920

See all PubMed Citations (5)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000113109.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	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		2	not provided	not provided	not provided

From GeneDx, SCV000170216.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From RettBASE, SCV000188072.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	No	curation	PubMed (4)
2	not provided	1	not provided	not provided	curation	PubMed (4)
3	not provided	1	not provided	not provided	curation	PubMed (4)
4	not provided	1	not provided	not provided	curation	PubMed (4)
5	not provided	1	not provided	not provided	curation	PubMed (4)
6	not provided	1	not provided	not provided	curation	PubMed (4)
7	not provided	1	not provided	not provided	curation	PubMed (4)

Description

Rett syndrome - not certain

"Rett syndrome - Not certain"

PubMed [ID: 10767337]

"Rett syndrome - Not certain"

PubMed [ID: 11055898]

"Not Rett synd. - autism spectrum disorder"

PubMed [ID: 20479760]

"Not Rett synd. - normal control"

PubMed [ID: 20479760]

"Not Rett synd. - schizophrenia"

PubMed [ID: 20479760]

"Rett syndrome - Not certain"

PubMed [ID: 21160487]

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	1	blood	not provided		1	not provided	not provided	not provided
2	unknown	not provided	1	Blood	not provided		1	not provided	not provided	not provided
3	unknown	not provided	1	not provided	not provided		1	not provided	not provided	not provided
4	unknown	not provided	1	blood, lymphoblastoid cell lin	not provided		1	not provided	not provided	not provided
5	unknown	not provided	1	blood, lymphoblastoid cell lin	not provided		1	not provided	not provided	not provided
6	unknown	not provided	1	blood, lymphoblastoid cell lin	not provided		1	not provided	not provided	not provided
7	unknown	not provided	1	blood	not provided		1	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV000247965.3

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital, SCV000257508.1

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

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

From PreventionGenetics, part of Exact Sciences, SCV000310760.1

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

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003800987.2

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

#	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: Oct 20, 2024

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