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.1186C>T (p.Pro396Ser)

CA10558495

589521 (ClinVar)

Gene: MECP2 (HGNC:4204)
Condition: Rett syndrome (MONDO:0010726)
Inheritance Mode: X-linked inheritance
UUID: e4bdbb3c-2c00-449e-a92f-3e252d0979be
Approved on: 2025-10-28
Published on: 2025-12-23

HGVS expressions

NM_001110792.2(MECP2):c.1186C>T (p.Pro396Ser)
NM_001110792.2:c.1186C>T
NC_000023.11:g.154030678G>A
CM000685.2:g.154030678G>A
NC_000023.10:g.153296129G>A
CM000685.1:g.153296129G>A
NC_000023.9:g.152949323G>A
NG_007107.2:g.111450C>T
NG_007107.3:g.111426C>T
ENST00000303391.11:c.1150C>T
ENST00000453960.7:c.1186C>T
ENST00000303391.10:c.1150C>T
ENST00000407218.5:c.*522C>T
ENST00000453960.6:c.1186C>T
ENST00000619732.4:c.1150C>T
ENST00000628176.2:c.*522C>T
NM_001110792.1:c.1186C>T
NM_001316337.1:c.871C>T
NM_004992.3:c.1150C>T
NM_001316337.2:c.871C>T
NM_001369391.2:c.871C>T
NM_001369392.2:c.871C>T
NM_001369393.2:c.871C>T
NM_001369394.1:c.871C>T
NM_001369394.2:c.871C>T
NM_001386137.1:c.481C>T
NM_001386138.1:c.481C>T
NM_001386139.1:c.481C>T
NM_004992.4:c.1150C>T
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Benign

Met criteria codes 2
BS2 BS1
Not Met criteria codes 2
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 5.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The highest population minor allele frequency of the p.Pro384Ser variant in MECP2 (NM_004992.4) in gnomAD v4.1.0 is 0.00001762 in the South Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0000083) for BS1, and therefore meets this criterion (BS1). The p.Pro384Ser variant is observed in at least 2 unaffected individuals (internal database - Labcorp (formerly Invitae); internal database - Ambry) (BS2). In summary, the p.Pro384Ser variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BS1, BS2). (MECP2 Specifications v5.0.0; curation approved on 10/28/2025)
Met criteria codes
BS2
The p.Pro384Ser variant is observed in at least 2 unaffected individuals (internal database - Labcorp (formerly Invitae); internal database - Ambry) (BS2).
BS1
The highest population minor allele frequency of the p.Pro384Ser variant in MECP2 (NM_004992.4) in gnomAD v4.1.0 is 0.00001762 in the South Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0000083) for BS1, and therefore meets this criterion (BS1).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL 0.424
Curation History
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