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.1042C>G (p.Leu348Val)

CA294661

156628 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
UUID: 17c62194-5666-4b79-956d-b912cd779fb1
Approved on: 2024-08-30
Published on: 2024-12-23

HGVS expressions

NM_001110792.2:c.1042C>G
NM_001110792.2(MECP2):c.1042C>G (p.Leu348Val)
NC_000023.11:g.154030822G>C
CM000685.2:g.154030822G>C
NC_000023.10:g.153296273G>C
CM000685.1:g.153296273G>C
NC_000023.9:g.152949467G>C
NG_007107.2:g.111306C>G
NG_007107.3:g.111282C>G
ENST00000303391.11:c.1006C>G
ENST00000453960.7:c.1042C>G
ENST00000303391.10:c.1006C>G
ENST00000407218.5:c.*378C>G
ENST00000453960.6:c.1042C>G
ENST00000619732.4:c.1006C>G
ENST00000628176.2:c.*378C>G
NM_001110792.1:c.1042C>G
NM_001316337.1:c.727C>G
NM_004992.3:c.1006C>G
NM_001316337.2:c.727C>G
NM_001369391.2:c.727C>G
NM_001369392.2:c.727C>G
NM_001369393.2:c.727C>G
NM_001369394.1:c.727C>G
NM_001369394.2:c.727C>G
NM_001386137.1:c.337C>G
NM_001386138.1:c.337C>G
NM_001386139.1:c.337C>G
NM_004992.4:c.1006C>G
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Benign

Met criteria codes 3
BA1 BP5_Strong BS2
Not Met criteria codes 1
PM2

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 highest population minor allele frequency of the p.Leu336Val variant in MECP2 (NM_004992.4) in gnomAD v4.1 is 0.001148 in the Middle Eastern population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The p.Leu336Val variant is observed in at least 2 unaffected individuals (internal database - GeneDx) (BS2). The p.Leu336Val variant is found in at least 3 patients with an alternate molecular basis of disease (internal database) (BP5_Strong). In summary, the p.Leu336Val variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP5_Strong). (MECP2 specification v3.0.0; curation approved on 8/30/2024)
Met criteria codes
BA1
The highest population minor allele frequency of the p.Leu336Val variant in MECP2 (NM_004992.4) in gnomAD v4.1 is 0.001148 in the Middle Eastern population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1).
BP5_Strong
The p.Leu336Val variant (NM_004992.4) is found in at least 3 patients with an alternate molecular basis of disease (internal database) (BP5_Strong).
BS2
The p.Leu336Val variant (NM_004992.4) is observed in at least 2 unaffected individuals (internal database - GeneDx) (BS2).
Not Met criteria codes
PM2
The p.Leu336Val variant in MECP2 (NM_004992.4) is absent from gnomAD v2 but present in gnomAD v4.1.
Curation History
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