Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_001110792.2(MECP2):c.1225G>A (p.Glu409Lys)

CA211306

95187 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 9117a511-01ac-4ea0-85db-858db41ea9d3

HGVS expressions

NM_001110792.2:c.1225G>A

NM_001110792.2(MECP2):c.1225G>A (p.Glu409Lys)

NC_000023.11:g.154030639C>T

CM000685.2:g.154030639C>T

NC_000023.10:g.153296090C>T

CM000685.1:g.153296090C>T

NC_000023.9:g.152949284C>T

NG_007107.2:g.111489G>A

NG_007107.3:g.111465G>A

ENST00000303391.11:c.1189G>A

ENST00000453960.7:c.1225G>A

ENST00000303391.10:c.1189G>A

ENST00000407218.5:c.*561G>A

ENST00000453960.6:c.1225G>A

ENST00000619732.4:c.1189G>A

ENST00000628176.2:c.*561G>A

NM_001110792.1:c.1225G>A

NM_001316337.1:c.910G>A

NM_004992.3:c.1189G>A

NM_001316337.2:c.910G>A

NM_001369391.2:c.910G>A

NM_001369392.2:c.910G>A

NM_001369393.2:c.910G>A

NM_001369394.1:c.910G>A

NM_001369394.2:c.910G>A

NM_001386137.1:c.520G>A

NM_001386138.1:c.520G>A

NM_001386139.1:c.520G>A

NM_004992.4:c.1189G>A

Benign

BA1 BS2

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The allele frequency of the p.Glu397Lys variant in MECP2 (NM_004992) is 0.393% in European (Non-Finnish) sub population in gnomAD, which is high enough to be classified as Benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Glu397Lys variant is observed in at least 2 unaffected individuals (PMID 10577905,12384770, RettBASE) (BS2). In summary, the p.Glu397Lys variant in MECP2 is classified as Benign based on the ACMG/AMP criteria applied (BA1, BS2).

BA1

The allele frequency of the p.(Glu397Lys) variant in MECP2 is 0.393% in European (Non-Finnish) sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.

BS2

The p.(Glu397Lys) variant is observed in at least 2 unaffected individuals (PMID 10577905,12384770, RettBASE)

Approved on: 2022-05-10

Published on: 2022-06-28

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