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.1458T>C (p.Pro486=)

CA519704534

516510 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 4b9145aa-2ae7-4e22-93bb-533ed5e9a32d
Approved on: 2024-04-18
Published on: 2025-03-13

HGVS expressions

NM_001110792.2:c.1458T>C
NM_001110792.2(MECP2):c.1458T>C (p.Pro486=)
NC_000023.11:g.154030406A>G
CM000685.2:g.154030406A>G
NC_000023.10:g.153295857A>G
CM000685.1:g.153295857A>G
NC_000023.9:g.152949051A>G
NG_007107.2:g.111722T>C
NG_007107.3:g.111698T>C
ENST00000303391.11:c.1422T>C
ENST00000453960.7:c.1458T>C
ENST00000303391.10:c.1422T>C
ENST00000453960.6:c.1458T>C
ENST00000619732.4:c.1422T>C
ENST00000628176.2:c.*794T>C
NM_001110792.1:c.1458T>C
NM_001316337.1:c.1143T>C
NM_004992.3:c.1422T>C
NM_001316337.2:c.1143T>C
NM_001369391.2:c.1143T>C
NM_001369392.2:c.1143T>C
NM_001369393.2:c.1143T>C
NM_001369394.1:c.1143T>C
NM_001369394.2:c.1143T>C
NM_001386137.1:c.753T>C
NM_001386138.1:c.753T>C
NM_001386139.1:c.753T>C
NM_004992.4:c.1422T>C
More

Likely Benign

Met criteria codes 3
BS2_Supporting BP5 BP4
Not Met criteria codes 2
BS1 PM2

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 p.Pro474= variant in MECP2 (NM_004992.3) in gnomAD v4.1 is 0.000008935 in European (Non-Finnish) population (not sufficient to meet BS1 criteria). The p.Pro474= variant is observed in at least 1 unaffected individual (GeneDx internal database) (BS2_supporting). The p.Pro474= variant is found in a patient with an alternate molecular basis of disease (GeneDx internal database) (BP5). Splice prediction analysis does not suggest an impact to splicing (BP4). In summary, the p.Pro474= variant in MECP2 is classified as likely benign based on the ACMG/AMP criteria (BS2_supporting, BP5, BP4).
Met criteria codes
BS2_Supporting
The p.Pro474= variant in MECP2 (NM_004992.3) is observed in at least 1 unaffected individual (GeneDx internal database).
BP5
The p.Pro474= variant in MECP2 (NM_004992.3) is found in a patient with an alternate molecular basis of disease (GeneDx internal database).
BP4
Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4).
Not Met criteria codes
BS1
The highest population minor allele frequency of the p.Pro474= variant in MECP2 (NM_004992.3) in gnomAD v4.1 is 0.000008935 in European (Non-Finnish) population (not sufficient to meet BS1 criteria).
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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