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]
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Variant: NM_001110792.2(MECP2):c.301C>T (p.Arg101Cys)

CA10558644

590069 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 896c2aa8-c0da-4847-9e70-9351eadce6d9
Approved on: 2024-04-18
Published on: 2024-07-01

HGVS expressions

NM_001110792.2:c.301C>T
NM_001110792.2(MECP2):c.301C>T (p.Arg101Cys)
NC_000023.11:g.154032319G>A
CM000685.2:g.154032319G>A
NC_000023.10:g.153297770G>A
CM000685.1:g.153297770G>A
NC_000023.9:g.152950964G>A
NG_007107.2:g.109809C>T
NG_007107.3:g.109785C>T
ENST00000303391.11:c.265C>T
ENST00000453960.7:c.301C>T
ENST00000303391.10:c.265C>T
ENST00000369957.5:c.*319C>T
ENST00000407218.5:c.301C>T
ENST00000453960.6:c.301C>T
ENST00000486506.5:n.2613C>T
ENST00000611468.1:c.253C>T
ENST00000619732.4:c.265C>T
ENST00000622433.4:c.253C>T
ENST00000628176.2:c.265C>T
NM_001110792.1:c.301C>T
NM_001316337.1:c.-15C>T
NM_004992.3:c.265C>T
NM_001316337.2:c.-15C>T
NM_001369391.2:c.-15C>T
NM_001369392.2:c.-15C>T
NM_001369393.2:c.-15C>T
NM_001369394.1:c.-15C>T
NM_001369394.2:c.-15C>T
NM_001386137.1:c.-296C>T
NM_001386138.1:c.-296C>T
NM_001386139.1:c.-296C>T
NM_004992.4:c.265C>T

Benign

Met criteria codes 2
BS2 BS1
Not Met criteria codes 1
BP4

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 allele frequency of the p.Arg89Cys variant in MECP2 (NM_004992.3) is 0.013% in Ashkenazi Jewish sub population in gnomAD v2.1.1, 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.Arg89Cys variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2). In summary, the p.Arg89Cys variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BS1, BS2).
Met criteria codes
BS2
The p.Arg89Cys variant is observed in at least 2 unaffected individuals (GeneDx internal database).
BS1
The allele frequency of the p.Arg89Cys variant in MECP2 (NM_004992.3) is 0.013% in Ashkenazi Jewish sub population in gnomAD v2.1.1, 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.
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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