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.1177C>T (p.Pro393Ser)

CA10558497

431897 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
UUID: 3fde14ce-243f-4159-b28d-83b15854bf43
Approved on: 2024-10-30
Published on: 2024-11-29

HGVS expressions

NM_001110792.2:c.1177C>T
NM_001110792.2(MECP2):c.1177C>T (p.Pro393Ser)
NC_000023.11:g.154030687G>A
CM000685.2:g.154030687G>A
NC_000023.10:g.153296138G>A
CM000685.1:g.153296138G>A
NC_000023.9:g.152949332G>A
NG_007107.2:g.111441C>T
NG_007107.3:g.111417C>T
ENST00000303391.11:c.1141C>T
ENST00000453960.7:c.1177C>T
ENST00000303391.10:c.1141C>T
ENST00000407218.5:c.*513C>T
ENST00000453960.6:c.1177C>T
ENST00000619732.4:c.1141C>T
ENST00000628176.2:c.*513C>T
NM_001110792.1:c.1177C>T
NM_001316337.1:c.862C>T
NM_004992.3:c.1141C>T
NM_001316337.2:c.862C>T
NM_001369391.2:c.862C>T
NM_001369392.2:c.862C>T
NM_001369393.2:c.862C>T
NM_001369394.1:c.862C>T
NM_001369394.2:c.862C>T
NM_001386137.1:c.472C>T
NM_001386138.1:c.472C>T
NM_001386139.1:c.472C>T
NM_004992.4:c.1141C>T
More

Likely Benign

Met criteria codes 2
BS2 BP5
Not Met criteria codes 4
PM1 BS1 BP4 PP3

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.Pro381Ser variant in MECP2 (NM_004992.4) is observed in at least 19 unaffected individuals (internal database - GeneDx, internal database - Invitae) (BS2). The p.Pro381Ser variant is found in a patient with an alternate molecular basis of disease (internal database - GeneDx) (BP5). The highest population minor allele frequency of the p.Pro381Ser variant in MECP2 in gnomAD v4.1 is 0.00003574 in the African/African American population (not sufficient to meet BS1 criteria). In summary, the p.Pro381Ser variant in MECP2 is classified as Likely Benign based on the ACMG/AMP criteria (BS2, BP5).
Met criteria codes
BS2
The p.Pro381Ser variant in MECP2 (NM_004992.4) is observed in at least 19 unaffected individuals (internal database - GeneDx, internal database - Invitae) (BS2).
BP5
The p.Pro381Ser variant is found in a patient with an alternate molecular basis of disease (internal database - GeneDx) (BP5).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The highest population minor allele frequency of the p.Pro381Ser variant in MECP2 in gnomAD v4.1 is 0.00003574 in the African/African American population (not sufficient to meet BS1 criteria).
BP4
The computational predictor REVEL gives a score of 0.451.
PP3
The computational predictor REVEL gives a score of 0.451.
Curation History
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