Variant: NM_004992.3(MECP2):c.1180G>A (p.Glu394Lys)

CA170197

143421 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

UUID: cb6d3431-d972-4851-bc8e-700dee1752ff

Approved on: 2021-03-26

Published on: 2021-05-17

HGVS expressions

NM_004992.3:c.1180G>A
NM_004992.3(MECP2):c.1180G>A (p.Glu394Lys)
ENST00000303391.11:c.1180G>A
ENST00000453960.7:c.1216G>A
ENST00000303391.10:c.1180G>A
ENST00000407218.5:c.*552G>A
ENST00000453960.6:c.1216G>A
ENST00000619732.4:c.1180G>A
ENST00000628176.2:c.*552G>A
NM_001110792.1:c.1216G>A
NM_001316337.1:c.901G>A
NM_001110792.2:c.1216G>A
NM_001316337.2:c.901G>A
NM_001369391.2:c.901G>A
NM_001369392.2:c.901G>A
NM_001369393.2:c.901G>A
NM_001369394.1:c.901G>A
NM_001369394.2:c.901G>A
NM_001386137.1:c.511G>A
NM_001386138.1:c.511G>A
NM_001386139.1:c.511G>A
NM_004992.4:c.1180G>A
NC_000023.11:g.154030648C>T
CM000685.2:g.154030648C>T
NC_000023.10:g.153296099C>T
CM000685.1:g.153296099C>T
NC_000023.9:g.152949293C>T
NG_007107.2:g.111480G>A
NG_007107.3:g.111456G>A

Benign

• Met criteria codes: BA1 BS2 BP5 BP4

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The allele frequency of the p.Glu394Lys variant in MECP2 is 0.035% in East Asian 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.Glu394Lys variant is observed in at least 2 unaffected individuals (internal database) (BS2). Computational analysis prediction tools suggest that the p.Glu394Lys variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). The p.Glu394Lys variant is found in a patient with an alternate molecular basis of disease (internal database) (BP5). In summary, the p.Glu394Lys variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP4, BP5).

Met criteria codes

• BA1: The allele frequency of the p.Glu394Lys variant in MECP2 is 0.035% in East Asian 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.Glu394Lys variant is observed in at least 2 unaffected individuals (internal database)
• BP5: The p.Glu394Lys variant is found in a patient with an alternate molecular basis of disease (internal database)
• BP4: Computational analysis prediction tools suggest that the p.Glu394Lys variant does not have a deleterious impact; however this information does not predict clinical significance on its own