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.895G>C (p.Ala299Pro)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA270538

143716 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 0f98a548-1dd4-40b1-8250-58006cc20cfc

Approved on: 2021-10-28

Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.895G>C

NM_001110792.2(MECP2):c.895G>C (p.Ala299Pro)

NC_000023.11:g.154030969C>G

CM000685.2:g.154030969C>G

NC_000023.10:g.153296420C>G

CM000685.1:g.153296420C>G

NC_000023.9:g.152949614C>G

NG_007107.2:g.111159G>C

NG_007107.3:g.111135G>C

ENST00000303391.11:c.859G>C

ENST00000453960.7:c.895G>C

ENST00000637917.1:n.66-33G>C

ENST00000303391.10:c.859G>C

ENST00000407218.5:c.*231G>C

ENST00000453960.6:c.895G>C

ENST00000619732.4:c.859G>C

ENST00000622433.4:c.847G>C

ENST00000628176.2:c.*231G>C

NM_001110792.1:c.895G>C

NM_001316337.1:c.580G>C

NM_004992.3:c.859G>C

NM_001316337.2:c.580G>C

NM_001369391.2:c.580G>C

NM_001369392.2:c.580G>C

NM_001369393.2:c.580G>C

NM_001369394.1:c.580G>C

NM_001369394.2:c.580G>C

NM_001386137.1:c.190G>C

NM_001386138.1:c.190G>C

NM_001386139.1:c.190G>C

NM_004992.4:c.859G>C

Likely Benign

BS2 BP5 BP2

PP4 PM1 BP4

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 p.Ala287Pro variant in MECP2 (NM_004992.3) is observed in at least 2 unaffected individuals (internal database - GeneDx, internal database - Baylor) (BS2). The p.Ala287Pro variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (internal database - GeneDx) (BP2). The p.Ala287Pro variant is found in a patient with an alternate molecular basis of disease (internal database - Baylor) (BP5). The p.Ala287Pro variant in MECP2 is present in gnomAD v2.1.1 at a frequency of 0.001638% (no criteria met). In summary, the p.Ala287Pro variant in MECP2 is classified as Likely Benign based on the ACMG/AMP criteria (BS2, BP2, BP5).

BS2

The p.Ala287Pro variant is observed in at least 2 unaffected individuals (internal database - GeneDx, internal database - Baylor) (BS2).

BP5

The p.Ala287Pro) variant is found in a patient with an alternate molecular basis of disease (internal database - Baylor) (BP5).

BP2

The p.Ala287Pro variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (internal database - GeneDx) (BP2).

PP4

The p.Ala287Pro variant in MECP2 was reported in PMID 11055898, a cohort of patients referred for MECP2 genetic testing with no specific clinical information available.

PM1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BP4

REVEL score 0.553 does not meet PP3 or BP4.

Curation History

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