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Variant: NM_001110792.2(MECP2):c.503A>G (p.Asp168Gly)

CA270431

143583 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
UUID: 1cb2470d-8a34-48e7-a854-6aae0154359d

HGVS expressions

NM_001110792.2:c.503A>G
NM_001110792.2(MECP2):c.503A>G (p.Asp168Gly)
NC_000023.11:g.154031361T>C
CM000685.2:g.154031361T>C
NC_000023.10:g.153296812T>C
CM000685.1:g.153296812T>C
NC_000023.9:g.152950006T>C
NG_007107.2:g.110767A>G
NG_007107.3:g.110743A>G
ENST00000303391.11:c.467A>G
ENST00000453960.7:c.503A>G
ENST00000637917.1:n.65+35A>G
ENST00000303391.10:c.467A>G
ENST00000407218.5:c.468+35A>G
ENST00000453960.6:c.503A>G
ENST00000486506.5:n.2815A>G
ENST00000611468.1:c.455A>G
ENST00000619732.4:c.467A>G
ENST00000622433.4:c.455A>G
ENST00000628176.2:c.432+35A>G
NM_001110792.1:c.503A>G
NM_001316337.1:c.188A>G
NM_004992.3:c.467A>G
NM_001316337.2:c.188A>G
NM_001369391.2:c.188A>G
NM_001369392.2:c.188A>G
NM_001369393.2:c.188A>G
NM_001369394.1:c.188A>G
NM_001369394.2:c.188A>G
NM_001386137.1:c.-129+35A>G
NM_001386138.1:c.-129+35A>G
NM_001386139.1:c.-129+35A>G
NM_004992.4:c.467A>G

Pathogenic

Met criteria codes 7
PP3 PM6_Strong PM2 PM5 PM1 PS3_Supporting PS4_Moderate
Not Met criteria codes 1
PP4

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 p.Asp156Gly variant in MECP2 (NM_004992.3) has been reported in at least 2 de novo occurrences (biological parentage unconfirmed) in individuals with phenotype consistent with Rett syndrome (PMID 11309679, 11241840) (PM6_strong). The p.Asp156Gly variant in MECP2 has been observed in at least 2 other individuals with clinical features of Rett syndrome (PMID 11309679, 11241840) (PS4_moderate). The p.Asp156Gly variant occurs in the well-characterized methyl-binding domain (MBD) functional domain of MECP2 (PMID 1326358, 23770565) (PM1). A pathogenic missense variant (p.Asp156Glu) has been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 11524741, 15737703, 26984561, 27354166, 12843318, 26418480, internal database - Invitae) (PM5). The p.Asp156Gly variant in MECP2 is absent from gnomAD (PM2_supporting). Chromatin binding and in vitro transcription repression assays have shown that this variant impacts protein function (PMID 12843318) (PS3_supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). In summary, the p.Asp156Gly variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PM6_strong, PS4_moderate, PM1, PM5, PS3_supporting, PM2_supporting, PP3).
Met criteria codes
PP3
Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3).
PM6_Strong
The p.Asp156Gly variant in MECP2 has been reported in at least 2 de novo occurrences (biological parentage unconfirmed) in individuals with Rett syndrome (PMID 11309679, 11241840) (PM6_strong, PP4).
PM2
The p.Asp156Gly variant in MECP2 is absent from gnomAD (PM2_supporting).
PM5
A pathogenic missense variant (p.Asp156Glu) has been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 11524741, 15737703, 26984561, 27354166, 12843318, 26418480, internal database - Invitae) (PM5).
PM1
The p.Asp156Gly variant occurs in the well-characterized methyl-binding domain (MBD) functional domain of MECP2 (PMID 1326358, 23770565) (PM1).
PS3_Supporting
Chromatin binding and in vitro transcription repression assays have shown that this variant impacts protein function (PMID 12843318).
PS4_Moderate
The p.Asp156Gly variant in MECP2 has been observed in at least 2 other individual2 with clinical features of Rett syndrome (PMID 11309679, 11241840) (PS4_moderate).
Not Met criteria codes
PP4
In PMID 11241840 the patient cohort was given a tentative diagnosis of Rett syndrome.
Approved on: 2021-10-26
Published on: 2021-12-27
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