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.1198_1215del (p.Pro400_Pro405del)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA170191

143396 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 3b395a01-a218-43cd-8c3a-a923a6649c44

Approved on: 2021-12-22

Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.1198_1215del

NM_001110792.2(MECP2):c.1198_1215del (p.Pro400_Pro405del)

NC_000023.11:g.154030653_154030670del

CM000685.2:g.154030653_154030670del

NC_000023.10:g.153296104_153296121del

CM000685.1:g.153296104_153296121del

NC_000023.9:g.152949298_152949315del

NG_007107.2:g.111462_111479del

NG_007107.3:g.111438_111455del

ENST00000303391.11:c.1162_1179del

ENST00000453960.7:c.1198_1215del

ENST00000303391.10:c.1162_1179del

ENST00000407218.5:c.*534_*551del

ENST00000453960.6:c.1198_1215del

ENST00000619732.4:c.1162_1179del

ENST00000628176.2:c.*534_*551del

NM_001110792.1:c.1198_1215del

NM_001316337.1:c.883_900del

NM_004992.3:c.1162_1179del

NM_001316337.2:c.883_900del

NM_001369391.2:c.883_900del

NM_001369392.2:c.883_900del

NM_001369393.2:c.883_900del

NM_001369394.1:c.883_900del

NM_001369394.2:c.883_900del

NM_001386137.1:c.493_510del

NM_001386138.1:c.493_510del

NM_001386139.1:c.493_510del

NM_004992.4:c.1162_1179del

Likely Benign

BS1 BP5 BS2_Supporting

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.Pro388_Pro393del (NM_004992.3) variant in MECP2 is 0.01% in the African/African American sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Pro388_Pro393del variant is observed in at least 1 unaffected individual (PMID 21160487)(BS2_supporting). The p.Pro388_Pro393del variant is found in a patient with an alternate molecular basis of disease (PMID 21160487)(BP5). In summary, the p.Pro388_Pro393del variant in MECP2 is classified as likely benign based on the ACMG/AMP criteria (BS1, BS2_supporting, BP5).

BS1

The allele frequency of the p.Pro388_Pro393del variant in MECP2 is .01% in the African/African American sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.

BP5

The p.Pro400_Pro405del variant is found in a patient with an alternate molecular basis of disease (PMID 21160487)

BS2_Supporting

The p.Pro400_Pro405del variant is observed in at least 1 unaffected individual (PMID 21160487)

Curation History

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