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]
  • See Evidence submitted by expert panel for details.

Variant: NM_001110792.2(MECP2):c.1A>T (p.Met1Leu)

CA274666

156661 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 8848c6dc-c0a0-47d8-9b94-3631b6b639b6
Approved on: 2021-12-22
Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.1A>T
NM_001110792.2(MECP2):c.1A>T (p.Met1Leu)
NC_000023.11:g.154097665T>A
CM000685.2:g.154097665T>A
NC_000023.10:g.153363122T>A
CM000685.1:g.153363122T>A
NC_000023.9:g.153016316T>A
NG_007107.2:g.44457A>T
NG_007107.3:g.44439A>T
ENST00000303391.11:c.-160A>T
ENST00000453960.7:c.1A>T
ENST00000303391.10:c.-160A>T
ENST00000407218.5:c.1A>T
ENST00000453960.6:c.1A>T
ENST00000619732.4:c.-160A>T
ENST00000627864.1:n.16A>T
ENST00000628176.2:c.-160A>T
ENST00000631210.1:n.305+7116A>T
NM_001110792.1:c.1A>T
NM_001316337.1:c.-607A>T
NM_004992.3:c.-160A>T
NM_001316337.2:c.-607A>T
NM_001369391.2:c.-902A>T
NM_001369392.2:c.-551A>T
NM_001369393.2:c.-427A>T
NM_001386137.1:c.-832A>T
NM_001386138.1:c.-720A>T
NM_001386139.1:c.-596A>T
NM_004992.4:c.-160A>T
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Likely Pathogenic

Met criteria codes 3
PP4 PM6_Strong PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Met1Leu variant (NM_001110792.2) in MECP2 has been reported in at least 2 de novo occurrences (biological parentage unconfirmed) in individuals with Rett syndrome (PMID 16225173, GeneDx Internal Database)(PM6_strong, PP4). The p.Met1Leu variant in MECP2 is absent from gnomAD (PM2_supporting). In summary, the p.Met1Leu variant in MECP2 is classified as a likely pathogenic variant based on the ACMG/AMP criteria (PM6_strong, PP4, PM2_supporting).
Met criteria codes
PP4
The p.Met1Leu variant in MECP2 has been reported in an individual with a clinical phenotype suggestive of Rett syndrome (PMID 16225173)
PM6_Strong
The pMet1Leu variant in MECP2 has been reported in at least 2 de novo occurrences (biological parentage unconfirmed) in individuals with Rett syndrome (PMID 16225173, GeneDx Internal Database)
PM2_Supporting
The p.Met1Leu variant in MECP2 is absent from gnomAD
Curation History
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