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NM_001110792.2(MECP2):c.626C>T (p.Thr209Met) AND Inborn genetic diseases

Germline classification:
Benign (1 submission)
Last evaluated:
Aug 4, 2017
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:
RCV002316387.9

Allele description [Variation Report for NM_001110792.2(MECP2):c.626C>T (p.Thr209Met)]

NM_001110792.2(MECP2):c.626C>T (p.Thr209Met)

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.626C>T (p.Thr209Met)
Other names:
p.T197M:ACG>ATG; NM_001110792.2(MECP2):c.626C>T
HGVS:
  • NC_000023.11:g.154031238G>A
  • NG_007107.3:g.110866C>T
  • NM_001110792.2:c.626C>TMANE SELECT
  • NM_001316337.2:c.311C>T
  • NM_001369391.2:c.311C>T
  • NM_001369392.2:c.311C>T
  • NM_001369393.2:c.311C>T
  • NM_001369394.2:c.311C>T
  • NM_001386137.1:c.-80C>T
  • NM_001386138.1:c.-80C>T
  • NM_001386139.1:c.-80C>T
  • NM_004992.4:c.590C>T
  • NP_001104262.1:p.Thr209Met
  • NP_001303266.1:p.Thr104Met
  • NP_001356320.1:p.Thr104Met
  • NP_001356321.1:p.Thr104Met
  • NP_001356322.1:p.Thr104Met
  • NP_001356323.1:p.Thr104Met
  • NP_004983.1:p.Thr197Met
  • NP_004983.1:p.Thr197Met
  • LRG_764t1:c.626C>T
  • LRG_764t2:c.590C>T
  • AJ132917.1:c.590C>T
  • LRG_764:g.110866C>T
  • LRG_764p1:p.Thr209Met
  • LRG_764p2:p.Thr197Met
  • NC_000023.10:g.153296689G>A
  • NG_007107.2:g.110890C>T
  • NM_001110792.1:c.626C>T
  • NM_004992.3:c.590C>T
  • P51608:p.Thr197Met
Protein change:
T104M
Links:
UniProtKB: P51608#VAR_018195; dbSNP: rs61749714
NCBI 1000 Genomes Browser:
rs61749714
Molecular consequence:
  • NM_001386137.1:c.-80C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-80C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-80C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.626C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.311C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.311C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.311C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.311C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.311C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000851917Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Benign
(Aug 4, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV000851917.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024