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]
x This classification has been retracted/unpublished!
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data

Variant: NM_001110792.2(MECP2):c.723G>T (p.Ser241=)

CA16608317

392584 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: bbe51f02-8137-456a-a7c8-400cccc59a29
Approved on: 2024-06-25
Published on: 2024-10-25

HGVS expressions

NM_001110792.2:c.723G>T
NM_001110792.2(MECP2):c.723G>T (p.Ser241=)
NC_000023.11:g.154031141C>A
CM000685.2:g.154031141C>A
NC_000023.10:g.153296592C>A
CM000685.1:g.153296592C>A
NC_000023.9:g.152949786C>A
NG_007107.2:g.110987G>T
NG_007107.3:g.110963G>T
ENST00000303391.11:c.687G>T
ENST00000453960.7:c.723G>T
ENST00000637917.1:c.66-205G>T
ENST00000303391.10:c.687G>T
ENST00000407218.5:c.*59G>T
ENST00000453960.6:c.723G>T
ENST00000619732.4:c.687G>T
ENST00000622433.4:c.675G>T
ENST00000628176.2:c.*59G>T
NM_001110792.1:c.723G>T
NM_001316337.1:c.408G>T
NM_004992.3:c.687G>T
NM_001316337.2:c.408G>T
NM_001369391.2:c.408G>T
NM_001369392.2:c.408G>T
NM_001369393.2:c.408G>T
NM_001369394.1:c.408G>T
NM_001369394.2:c.408G>T
NM_001386137.1:c.18G>T
NM_001386138.1:c.18G>T
NM_001386139.1:c.18G>T
NM_004992.4:c.687G>T
More

Likely Benign

Met criteria codes 4
BP4 BP5 BP7 BS2_Supporting
Not Met criteria codes 2
BS1 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MECP2 Version 3.0.0

Criteria Specification Approval History
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.Ser229= variant in MECP2 (NM_004992.4) in gnomAD v4.1 is 0.000028 in the European (non-Finnish) population (not sufficient to meet BS1 criteria). The p.Ser229= variant is observed in at least 1 unaffected individual (Internal database - Invitae) (BS2_Supporting). The p.Ser229= variant is found in a patient with an alternate molecular basis of disease (Internal database - Invitae) (BP5). The silent p.Ser229= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). In summary, the p.Ser229= variant in MECP2 is classified as a likely benign variant based on the ACMG/AMP criteria (BS2_Supporting, BP5, BP4, BP7).
Met criteria codes
BP4
The silent p.Ser229= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4).
BP5
The p.Ser229= variant is found in a patient with an alternate molecular basis of disease (Internal database - Invitae).
BP7
The silent p.Ser229= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7).
BS2_Supporting
The p.Ser229= variant is observed in at least 1 unaffected individuals (Internal database - Invitae).
Not Met criteria codes
BS1
The highest population minor allele frequency of the p.Ser229= variant in MECP2 in gnomAD v4.1 is 0.000028 in the European (non-Finnish) population (not sufficient to meet BS1 criteria).
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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