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]

Variant: NM_001110792.2(MECP2):c.1197_1202del (p.Pro402_Pro403del)

Curation Version - 1.0
Curation History
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CA232911

143390 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 51fcef87-f89a-413b-a5b7-0fe0d70aee75

Approved on: 2022-10-11

Published on: 2022-12-02

HGVS expressions

NM_001110792.2:c.1197_1202del

NM_001110792.2(MECP2):c.1197_1202del (p.Pro402_Pro403del)

NC_000023.11:g.154030664_154030669del

CM000685.2:g.154030664_154030669del

NC_000023.10:g.153296115_153296120del

CM000685.1:g.153296115_153296120del

NC_000023.9:g.152949309_152949314del

NG_007107.2:g.111461_111466del

NG_007107.3:g.111437_111442del

ENST00000303391.11:c.1161_1166del

ENST00000453960.7:c.1197_1202del

ENST00000303391.10:c.1161_1166del

ENST00000407218.5:c.*533_*538del

ENST00000453960.6:c.1197_1202del

ENST00000619732.4:c.1161_1166del

ENST00000628176.2:c.*533_*538del

NM_001110792.1:c.1197_1202del

NM_001316337.1:c.882_887del

NM_004992.3:c.1161_1166del

NM_001316337.2:c.882_887del

NM_001369391.2:c.882_887del

NM_001369392.2:c.882_887del

NM_001369393.2:c.882_887del

NM_001369394.1:c.882_887del

NM_001369394.2:c.882_887del

NM_001386137.1:c.492_497del

NM_001386138.1:c.492_497del

NM_001386139.1:c.492_497del

NM_004992.4:c.1161_1166del

Benign

BA1 BP2

PP4

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 p.Pro390_Pro391del variant in MECP2 (NM_004992.3) has been reported in an individual with intellectual disability (PMID 21982064). The allele frequency of the p.Pro390_Pro391del variant in MECP2 is 0.1158% in the South 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.Pro390_Pro391del variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (PMID: 23696494) (BP2). In summary, the p.Pro390_Pro391del variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BA1, BP2).

BA1

The allele frequency of the p.Pro390_Pro391del variant in MECP2 is 0.1158% in the South 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).

BP2

The p.Pro390_Pro391del variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (PMID: 23696494) (BP2).

PP4

The p.Pro390_Pro391del variant in MECP2 has been reported in an individual with intellectual disability (PMID 21982064).

Curation History

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