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 related information was provided by the message!
  • No CSPEC computed assertion could be determined for this classification!
  • See Evidence submitted by expert panel for details.

Variant: NM_001110792.2(MECP2):c.1169C>G (p.Ala390Gly)

CA270202

143340 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: cf528a11-2c85-4e05-8886-8ad74ebf5159
Approved on: 2022-10-11
Published on: 2022-12-02

HGVS expressions

NM_001110792.2:c.1169C>G
NM_001110792.2(MECP2):c.1169C>G (p.Ala390Gly)
NC_000023.11:g.154030695G>C
CM000685.2:g.154030695G>C
NC_000023.10:g.153296146G>C
CM000685.1:g.153296146G>C
NC_000023.9:g.152949340G>C
NG_007107.2:g.111433C>G
NG_007107.3:g.111409C>G
ENST00000303391.11:c.1133C>G
ENST00000453960.7:c.1169C>G
ENST00000303391.10:c.1133C>G
ENST00000407218.5:c.*505C>G
ENST00000453960.6:c.1169C>G
ENST00000619732.4:c.1133C>G
ENST00000628176.2:c.*505C>G
NM_001110792.1:c.1169C>G
NM_001316337.1:c.854C>G
NM_004992.3:c.1133C>G
NM_001316337.2:c.854C>G
NM_001369391.2:c.854C>G
NM_001369392.2:c.854C>G
NM_001369393.2:c.854C>G
NM_001369394.1:c.854C>G
NM_001369394.2:c.854C>G
NM_001386137.1:c.464C>G
NM_001386138.1:c.464C>G
NM_001386139.1:c.464C>G
NM_004992.4:c.1133C>G
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Uncertain Significance

Met criteria codes 2
PS4_Moderate BS2
Not Met criteria codes 4
PP4 PM1 BS1 BP4

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.Ala378Gly variant has been observed in 3 individuals with Rett syndrome (PMID 16473305, 20031356, 11960578) (PS4_moderate). The p.Ala378Gly variant is observed in at least 7 unaffected individuals (internal database - GeneDx; internal database - Invitae) (BS2). The p.Ala378Gly variant in MECP2 is present in 3 female and 1 male individual(s) in gnomAD (0.002%) (not sufficient to meet BS1 criteria). In summary, the p.Ala378Gly variant in MECP2 is classified as a Variant of Uncertain Significance based on the ACMG/AMP criteria (BS2, PS4_moderate).
Met criteria codes
PS4_Moderate
The p.Ala378Gly variant has been observed in 3 individuals with Rett syndrome (PMID: 16473305, 20031356, 11960578) (PS4_moderate).
BS2
The p.Ala378Gly variant is observed in at least 2 unaffected individuals (internal database - GeneDx; internal database - Invitae) (BS2).
Not Met criteria codes
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Allele frequency 0.00007 in Latino sub population. Does not meet BS1 requirements.
BP4
REVEL score 0.554.
Curation History
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