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]
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Variant: NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu)

CA170185

143383 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 2895aad2-34d6-4d56-8c6b-e11d15c61d64
Approved on: 2021-12-13
Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.1196C>T
NM_001110792.2(MECP2):c.1196C>T (p.Pro399Leu)
NC_000023.11:g.154030668G>A
CM000685.2:g.154030668G>A
NC_000023.10:g.153296119G>A
CM000685.1:g.153296119G>A
NC_000023.9:g.152949313G>A
NG_007107.2:g.111460C>T
NG_007107.3:g.111436C>T
ENST00000303391.11:c.1160C>T
ENST00000453960.7:c.1196C>T
ENST00000303391.10:c.1160C>T
ENST00000407218.5:c.*532C>T
ENST00000453960.6:c.1196C>T
ENST00000619732.4:c.1160C>T
ENST00000628176.2:c.*532C>T
NM_001110792.1:c.1196C>T
NM_001316337.1:c.881C>T
NM_004992.3:c.1160C>T
NM_001316337.2:c.881C>T
NM_001369391.2:c.881C>T
NM_001369392.2:c.881C>T
NM_001369393.2:c.881C>T
NM_001369394.1:c.881C>T
NM_001369394.2:c.881C>T
NM_001386137.1:c.491C>T
NM_001386138.1:c.491C>T
NM_001386139.1:c.491C>T
NM_004992.4:c.1160C>T

Benign

Met criteria codes 2
BS1 BS2

Evidence Links 0

Expert Panel

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.Pro387Leu (NM_004992.3) variant in MECP2 is 0.026% in South Asian sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Pro387Leu variant is observed in at least 2 unaffected individuals (PMID 12161600, GeneDx internal database) (BS2). In summary, the p.Pro387Leu variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BS1, BS2).
Met criteria codes
BS1
The allele frequency of the p.Pro399Leu variant in MECP2 is 0.026% in South Asian sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.
BS2
The p.Pro399Leu variant is observed in at least 2 unaffected individuals (PMID 12161600, GeneDx internal database)
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