NM_001110792.2(MECP2):c.631C>A (p.Pro211Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 17, 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:: RCV003230754.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.631C>A (p.Pro211Thr)]

NM_001110792.2(MECP2):c.631C>A (p.Pro211Thr)

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.631C>A (p.Pro211Thr)

HGVS:

NC_000023.11:g.154031233G>T
NG_007107.3:g.110871C>A
NM_001110792.2:c.631C>AMANE SELECT
NM_001316337.2:c.316C>A
NM_001369391.2:c.316C>A
NM_001369392.2:c.316C>A
NM_001369393.2:c.316C>A
NM_001369394.2:c.316C>A
NM_001386137.1:c.-75C>A
NM_001386138.1:c.-75C>A
NM_001386139.1:c.-75C>A
NM_004992.3:c.595C>A
NM_004992.4:c.595C>A
NP_001104262.1:p.Pro211Thr
NP_001303266.1:p.Pro106Thr
NP_001356320.1:p.Pro106Thr
NP_001356321.1:p.Pro106Thr
NP_001356322.1:p.Pro106Thr
NP_001356323.1:p.Pro106Thr
NP_004983.1:p.Pro199Thr
LRG_764t1:c.631C>A
LRG_764t2:c.595C>A
LRG_764:g.110871C>A
LRG_764p1:p.Pro211Thr
LRG_764p2:p.Pro199Thr
NC_000023.10:g.153296684G>T

Protein change:

P106T

Molecular consequence:

NM_001386137.1:c.-75C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386138.1:c.-75C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386139.1:c.-75C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001110792.2:c.631C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001316337.2:c.316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369391.2:c.316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369392.2:c.316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369393.2:c.316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369394.2:c.316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004992.4:c.595C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003929386	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 17, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003929386

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 17, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003929386.1

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

Description

Variant summary: MECP2 c.595C>A (p.Pro199Thr) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.5e-06 in 183435 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.595C>A in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Sep 29, 2024

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