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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • cspecId property did not resolve into a valid CSPEC request: https://cspec.genome.network/cspec-priv/SequenceVariantInterpretation/id/643243106!
  • cspec.ruleSetIri property did not resolve into a valid CSPEC request: https://cspec.genome.network/cspec-priv/RuleSet/id/643243113!
  • See Evidence submitted by expert panel for details.

Variant: NM_001110792.2(MECP2):c.6CGC[4] (p.Ala7_Ala8del)

CA199499

156657 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: b58e31c2-f4e0-4cf0-bc92-ecf79c6554fa
Approved on: 2024-04-18
Published on: 2025-03-13

HGVS expressions

NM_001110792.2:c.6CGC[4]
NM_001110792.2(MECP2):c.6CGC[4] (p.Ala7_Ala8del)
NC_000023.11:g.154097657_154097662del
CM000685.2:g.154097657_154097662del
NC_000023.10:g.153363114_153363119del
CM000685.1:g.153363114_153363119del
NC_000023.9:g.153016308_153016313del
NG_007107.2:g.44474_44479del
NG_007107.3:g.44456_44461del
ENST00000303391.11:c.-143_-138del
ENST00000453960.7:c.18_23del
ENST00000303391.10:c.-143_-138del
ENST00000369957.5:c.-143_-138del
ENST00000407218.5:c.18_23del
ENST00000453960.6:c.18_23del
ENST00000619732.4:c.-143_-138del
ENST00000627864.1:n.33_38del
ENST00000628176.2:c.-143_-138del
ENST00000631210.1:n.305+7133_305+7138del
NM_001110792.1:c.18_23del
NM_001316337.1:c.-590_-585del
NM_004992.3:c.-143_-138del
NM_001110792.2:c.18_23del
NM_001316337.2:c.-590_-585del
NM_001369391.2:c.-885_-880del
NM_001369392.2:c.-534_-529del
NM_001369393.2:c.-410_-405del
NM_001386137.1:c.-815_-810del
NM_001386138.1:c.-703_-698del
NM_001386139.1:c.-579_-574del
NM_004992.4:c.-143_-138del
More

Likely Benign

Met criteria codes 2
BS1 BP3
Not Met criteria codes 1
PS4

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 highest population minor allele frequency of the c.-143_-138del variant in MECP2 (NM_004992.4) in gnomAD v4.0 is 0.0001412 in the African/African American population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.00008) for BS1, and therefore meets this criterion (BS1). Larger deletions encompassing this region (c.-143_-138del) have been observed in an unaffected mother and father (Invitae internal database) (BP3). This variant has been observed in an individual with neurodevelopment disorder (PMID 1717659) (not sufficient for PS4_supporting). In summary, the c.-143_-138del variant in MECP2 is classified as likely benign based on the ACMG/AMP criteria (BS1, BP3).
Met criteria codes
BS1
The highest population minor allele frequency of the c.-143_-138del variant in MECP2 (NM_004992.4) in gnomAD v4.0 is 0.0001412 in the African/African American population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.00008) for BS1, and therefore meets this criterion (BS1).
BP3
Larger deletions encompassing this region (c.-143_-138del) have been observed in an unaffected mother and father (Invitae internal database) (BP3).
Not Met criteria codes
PS4
This variant has been observed in an individual with neurodevelopment disorder (PMID 1717659) (not sufficient for PS4_supporting).
Curation History
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