NM_001110792.2(MECP2):c.1176G>A (p.Val392=) AND Rett syndrome

Clinical significance:Benign (Last evaluated: Mar 26, 2021)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001110792.2(MECP2):c.1176G>A (p.Val392=)]

NM_001110792.2(MECP2):c.1176G>A (p.Val392=)

MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.1176G>A (p.Val392=)
Other names:
  • NC_000023.11:g.154030688C>T
  • NG_007107.2:g.111440G>A
  • NG_007107.3:g.111416G>A
  • NM_001110792.2:c.1176G>AMANE SELECT
  • NM_001316337.2:c.861G>A
  • NM_001369391.2:c.861G>A
  • NM_001369392.2:c.861G>A
  • NM_001369393.2:c.861G>A
  • NM_001369394.2:c.861G>A
  • NM_001386137.1:c.471G>A
  • NM_001386138.1:c.471G>A
  • NM_001386139.1:c.471G>A
  • NM_004992.3:c.1140G>A
  • NM_004992.4:c.1140G>A
  • NP_001104262.1:p.Val392=
  • NP_001303266.1:p.Val287=
  • NP_001356320.1:p.Val287=
  • NP_001356321.1:p.Val287=
  • NP_001356322.1:p.Val287=
  • NP_001356323.1:p.Val287=
  • NP_001373066.1:p.Val157=
  • NP_001373067.1:p.Val157=
  • NP_001373068.1:p.Val157=
  • NP_004983.1:p.Val380=
  • NP_004983.1:p.Val380=
  • LRG_764t1:c.1176G>A
  • LRG_764t2:c.1140G>A
  • LRG_764:g.111416G>A
  • LRG_764p1:p.Val392=
  • LRG_764p2:p.Val380=
  • NC_000023.10:g.153296139C>T
  • NM_004992.3(MECP2):c.1140G>A
  • p.Val380=
dbSNP: rs201711454
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001110792.2:c.1176G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001316337.2:c.861G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369391.2:c.861G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369392.2:c.861G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369393.2:c.861G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369394.2:c.861G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386137.1:c.471G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386138.1:c.471G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386139.1:c.471G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004992.3:c.1140G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004992.4:c.1140G>A - synonymous variant - [Sequence Ontology: SO:0001819]


Rett syndrome (RTT)
Autism, dementia, ataxia, and loss of purposeful hand use; MECP2-Related Disorders; Rett's disorder
MONDO: MONDO:0010726; MedGen: C0035372; Orphanet: 3095; Orphanet: 778; OMIM: 312750

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001711992ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel, ClinGenreviewed by expert panel
(Mar 26, 2021)

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel, ClinGen, SCV001711992.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided


The allele frequency of the p.Val380= variant in MECP2 is 0.018% in Latino sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Val380= variant is observed in at least 2 unaffected individuals (internal database) (BS2). The silent p.Val380= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). In summary, the p.Val380= variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BS1, BS2, BP7).

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

Last Updated: Nov 27, 2021

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