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 computer assertion could be determined for this classification!

Variant: NM_001110792.2(MECP2):c.1171C>T (p.Pro391Ser)

CA10558498

1170846 (ClinVar)

Gene: MECP2 (HGNC:4204)
Condition: Rett syndrome (MONDO:0010726)
Inheritance Mode: X-linked inheritance
UUID: 7d00b5af-dc6e-4fa1-b2c9-abb6ae37ead2
Approved on: 2024-02-23
Published on: 2024-06-27

HGVS expressions

NM_001110792.2:c.1171C>T
NM_001110792.2(MECP2):c.1171C>T (p.Pro391Ser)
NC_000023.11:g.154030693G>A
CM000685.2:g.154030693G>A
NC_000023.10:g.153296144G>A
CM000685.1:g.153296144G>A
NC_000023.9:g.152949338G>A
NG_007107.2:g.111435C>T
NG_007107.3:g.111411C>T
ENST00000303391.11:c.1135C>T
ENST00000453960.7:c.1171C>T
ENST00000303391.10:c.1135C>T
ENST00000407218.5:c.*507C>T
ENST00000453960.6:c.1171C>T
ENST00000619732.4:c.1135C>T
ENST00000628176.2:c.*507C>T
NM_001110792.1:c.1171C>T
NM_001316337.1:c.856C>T
NM_004992.3:c.1135C>T
NM_001316337.2:c.856C>T
NM_001369391.2:c.856C>T
NM_001369392.2:c.856C>T
NM_001369393.2:c.856C>T
NM_001369394.1:c.856C>T
NM_001369394.2:c.856C>T
NM_001386137.1:c.466C>T
NM_001386138.1:c.466C>T
NM_001386139.1:c.466C>T
NM_004992.4:c.1135C>T
More

Benign

Met criteria codes 3
BS1 BS2 BP5
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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The allele frequency of the p.Pro379Ser variant in MECP2 (NM_004992.3) is 0.017% in African sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Pro379Ser variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx, internal database - Invitae) (BS2). The p.Pro379Ser variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx, internal database - Invitae) (BP5). In summary, the p.Pro379Ser variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BS1, BS2, BP5).
Met criteria codes
BS1
The allele frequency of the p.Pro379Ser variant in MECP2 (NM_004992.3) is 0.017% in African/African American sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).
BS2
The p.Pro379Ser variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx, internal database - Invitae) (BS2).
BP5
The p.Pro379Ser variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx, internal database - Invitae) (BP5).
Not Met criteria codes
BP4
Computational prediction analysis tools are inconclusive for this variant (no criteria met).
PP3
Computational prediction analysis tools are inconclusive for this variant (no criteria met).
Curation History
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