Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001110792.2(MECP2):c.872C>T (p.Ala291Val)

CA270535

143710 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 073e9a0d-f2cc-49d2-bf45-62947b3c21a3
Approved on: 2024-10-30
Published on: 2024-11-29

HGVS expressions

NM_001110792.2:c.872C>T
NM_001110792.2(MECP2):c.872C>T (p.Ala291Val)
NC_000023.11:g.154030992G>A
CM000685.2:g.154030992G>A
NC_000023.10:g.153296443G>A
CM000685.1:g.153296443G>A
NC_000023.9:g.152949637G>A
NG_007107.2:g.111136C>T
NG_007107.3:g.111112C>T
ENST00000303391.11:c.836C>T
ENST00000453960.7:c.872C>T
ENST00000637917.1:c.66-56C>T
ENST00000303391.10:c.836C>T
ENST00000407218.5:c.*208C>T
ENST00000453960.6:c.872C>T
ENST00000619732.4:c.836C>T
ENST00000622433.4:c.824C>T
ENST00000628176.2:c.*208C>T
NM_001110792.1:c.872C>T
NM_001316337.1:c.557C>T
NM_004992.3:c.836C>T
NM_001316337.2:c.557C>T
NM_001369391.2:c.557C>T
NM_001369392.2:c.557C>T
NM_001369393.2:c.557C>T
NM_001369394.1:c.557C>T
NM_001369394.2:c.557C>T
NM_001386137.1:c.167C>T
NM_001386138.1:c.167C>T
NM_001386139.1:c.167C>T
NM_004992.4:c.836C>T
More

Likely Pathogenic

Met criteria codes 3
PS4 PP4 PM2_Supporting
Not Met criteria codes 3
BP4 PP3 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MECP2 Version 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Ala279Val variant in MECP2 (NM_004992.4) has been observed in at least 5 individuals with a clinical phenotype consistent with Rett syndrome (PMID: 15526954, ClinVar, internal database - Invitae) (PS4, PP4). The p.Ala279Val variant in MECP2 is absent from gnomAD v4.1 (PM2_Supporting). In summary, the p.Ala279Val variant in MECP2 is classified as Likely Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS4, PM2_supporting, PP4).
Met criteria codes
PS4
The p.Ala279Val variant has been observed in at least 5 individuals with a clinical phenotype consistent with Rett syndrome (PMID: 15526954, ClinVar, internal database - Invitae) (PS4).
PP4
The p.Ala279Val variant in MECP2 (NM_004992.4) has been reported in an individual with a clinical phenotype suggestive of Rett syndrome (PMID: 15526954) (PP4).
PM2_Supporting
The p.Ala279Val variant in MECP2 (NM_004992.4) is absent from gnomAD v4.1 (PM2_Supporting).
Not Met criteria codes
BP4
REVEL: 0.492 Computational prediction analysis tools are inconclusive for this variant.
PP3
REVEL: 0.492
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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