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Variant: NM_001110792.2(MECP2):c.1187C>T (p.Pro396Leu)

CA199482

36490 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
UUID: 38bf9f2d-64c8-4429-bc26-54f824404001
Approved on: 2023-03-27
Published on: 2023-03-31

HGVS expressions

NM_001110792.2:c.1187C>T
NM_001110792.2(MECP2):c.1187C>T (p.Pro396Leu)
NC_000023.11:g.154030677G>A
CM000685.2:g.154030677G>A
NC_000023.10:g.153296128G>A
CM000685.1:g.153296128G>A
NC_000023.9:g.152949322G>A
NG_007107.2:g.111451C>T
NG_007107.3:g.111427C>T
ENST00000303391.11:c.1151C>T
ENST00000453960.7:c.1187C>T
ENST00000303391.10:c.1151C>T
ENST00000407218.5:c.*523C>T
ENST00000453960.6:c.1187C>T
ENST00000619732.4:c.1151C>T
ENST00000628176.2:c.*523C>T
NM_001110792.1:c.1187C>T
NM_001316337.1:c.872C>T
NM_004992.3:c.1151C>T
NM_001316337.2:c.872C>T
NM_001369391.2:c.872C>T
NM_001369392.2:c.872C>T
NM_001369393.2:c.872C>T
NM_001369394.1:c.872C>T
NM_001369394.2:c.872C>T
NM_001386137.1:c.482C>T
NM_001386138.1:c.482C>T
NM_001386139.1:c.482C>T
NM_004992.4:c.1151C>T

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 3
PM6 BS2 BP5
Not Met criteria codes 2
BS1 PS4

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.Pro384Leu variant in MECP2 (NM_004992.3) has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with a neurological condition (PMID 22277191) (PM6). The p.Pro384Leu variant has been observed in 1 additional individual with intellectual disability (PMID 22277191) (not sufficient to meet PS4_supporting criteria). The p.Pro384Leu variant is observed in at least 8 unaffected individuals, most of whom are male (internal database - GeneDx; internal database - Invitae) (BS2). The p.Pro384Leu variant is found in a patient with an alternate molecular basis of disease (internal database - Invitae) (BP5). The p.Pro384Leu variant in MECP2 is present in 2 female individual(s) in gnomAD (0.0012%) (not sufficient to meet BS1 criteria). In summary, this variant meets the criteria to be classified as Likely Benign. Although there are both pathogenic and benign types of evidence for this variant, the pathogenic evidence is not considered inconsistent with the final classification. ACMG/AMP criteria applied, as specified by the ClinGen Rett/Angelman-like expert panel: PM6, BS2, BP5 (ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2; date of approval 12/13/2021).
Met criteria codes
PM6
The p.Pro384Leu variant in MECP2 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with a neurological condition (PMID 22277191) (PM6).
BS2
The p.Pro384Leu variant is observed in at least 8 unaffected individuals, most of whom were male (internal database - GeneDx; internal database - Invitae) (BS2).
BP5
The p.Pro384Leu variant is found in a patient with an alternate molecular basis of disease (internal database - Invitae) (BP5).
Not Met criteria codes
BS1
Allele frequency in Latino subpopulation is 0.00007; does not meet BS1.
PS4
The p.Pro384Leu variant has been observed in at least 1 individual with non-specific intellectual disability (PMID 22277191) (PS4_supporting not met).
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