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

Variant: NM_001110792.2(MECP2):c.1214C>T (p.Pro405Leu)

CA232923

143418 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 2983b3c7-626e-495d-81be-dcdb05e3c83d
Approved on: 2024-10-30
Published on: 2024-11-29

HGVS expressions

NM_001110792.2:c.1214C>T
NM_001110792.2(MECP2):c.1214C>T (p.Pro405Leu)
NC_000023.11:g.154030650G>A
CM000685.2:g.154030650G>A
NC_000023.10:g.153296101G>A
CM000685.1:g.153296101G>A
NC_000023.9:g.152949295G>A
NG_007107.2:g.111478C>T
NG_007107.3:g.111454C>T
ENST00000303391.11:c.1178C>T
ENST00000453960.7:c.1214C>T
ENST00000303391.10:c.1178C>T
ENST00000407218.5:c.*550C>T
ENST00000453960.6:c.1214C>T
ENST00000619732.4:c.1178C>T
ENST00000628176.2:c.*550C>T
NM_001110792.1:c.1214C>T
NM_001316337.1:c.899C>T
NM_004992.3:c.1178C>T
NM_001316337.2:c.899C>T
NM_001369391.2:c.899C>T
NM_001369392.2:c.899C>T
NM_001369393.2:c.899C>T
NM_001369394.1:c.899C>T
NM_001369394.2:c.899C>T
NM_001386137.1:c.509C>T
NM_001386138.1:c.509C>T
NM_001386139.1:c.509C>T
NM_004992.4:c.1178C>T
More

Likely Benign

Met criteria codes 2
BS2 BP5
Not Met criteria codes 5
BS1 BP4 PP3 PP4 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.Pro393Leu variant in MECP2 (NM_004992.4) is observed in at least 2 unaffected individuals (internal database - Ambry, internal database - Invitae) (BS2). The p.Pro393Leu variant is found in a patient with an alternate molecular basis of disease (internal database - Ambry) (BP5). The highest population minor allele frequency of the p.Pro393Leu variant in MECP2 in gnomAD v4.1 is 0.00002210 in Admixed American population (not sufficient to meet BS1 criteria). In summary, the p.Pro393Leu variant in MECP2 is classified as Likely Benign based on the ACMG/AMP criteria (BS2, BP5).
Met criteria codes
BS2
The p.Pro393Leu variant is observed in at least 2 unaffected individuals (internal database - Ambry, internal database - Invitae) (BS2).
BP5
The p.Pro393Leu variant is found in a patient with an alternate molecular basis of disease (internal database - Ambry) (BP5).
Not Met criteria codes
BS1
The highest population minor allele frequency of the p.Pro393Leu variant in MECP2 (NM_004992.4) in gnomAD v4.1 is 0.00002210 in Admixed American population (not sufficient to meet BS1 criteria).
BP4
The computational predictor REVEL gives a score of 0.38.
PP3
The computational predictor REVEL gives a score of 0.38.
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
Curation History
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