rs267608622

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NM_001110792.2(MECP2):​c.1324C>T​(p.Pro442Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,097,836 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: not found (cov: 22)
Exomes 𝑓: 0.000011 ( 0 hom. 3 hem. )

Consequence

MECP2
NM_001110792.2 missense

Scores

5
12

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.50
Variant links:
Genes affected
MECP2 (HGNC:6990): (methyl-CpG binding protein 2) DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.21211839).
BP6
Variant X-154030540-G-A is Benign according to our data. Variant chrX-154030540-G-A is described in ClinVar as [Benign]. Clinvar id is 143456.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154030540-G-A is described in Lovd as [Benign].
BS2
High Hemizygotes in GnomAdExome4 at 3 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MECP2NM_001110792.2 linkuse as main transcriptc.1324C>T p.Pro442Ser missense_variant 3/3 ENST00000453960.7 NP_001104262.1 P51608-2A0A140VKC4Q59FJ6
MECP2NM_004992.4 linkuse as main transcriptc.1288C>T p.Pro430Ser missense_variant 4/4 ENST00000303391.11 NP_004983.1 P51608-1D3YJ43Q59FJ6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MECP2ENST00000453960.7 linkuse as main transcriptc.1324C>T p.Pro442Ser missense_variant 3/31 NM_001110792.2 ENSP00000395535.2 P51608-2
MECP2ENST00000303391.11 linkuse as main transcriptc.1288C>T p.Pro430Ser missense_variant 4/41 NM_004992.4 ENSP00000301948.6 P51608-1
MECP2ENST00000628176 linkuse as main transcriptc.*660C>T 3_prime_UTR_variant 5/53 ENSP00000486978.1 A0A0D9SFX7

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD3 exomes
AF:
0.0000164
AC:
3
AN:
182893
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67407
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000722
Gnomad SAS exome
AF:
0.0000524
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000109
AC:
12
AN:
1097836
Hom.:
0
Cov.:
32
AF XY:
0.00000826
AC XY:
3
AN XY:
363240
show subpopulations
Gnomad4 AFR exome
AF:
0.0000758
Gnomad4 AMR exome
AF:
0.0000284
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000831
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
Cov.:
22
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Severe neonatal-onset encephalopathy with microcephaly Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpSep 08, 2023- -
not specified Benign:1
Benign, no assertion criteria providedcurationRettBASEMar 29, 2011- -
Rett syndrome Benign:1
Benign, criteria provided, single submittercurationCentre for Population Genomics, CPGMar 13, 2024This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as benign. At least the following criteria are met: The variant is observed in at least 2 individuals with no features of Rett Syndrome (BS2).PMID: 21285040 The allele frequency of this variant in at least one population in gnomAD is between 0.008% and 0.03% (BS1). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.094
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Uncertain
-0.020
CADD
Benign
18
DANN
Benign
0.96
DEOGEN2
Benign
0.25
T;.
FATHMM_MKL
Benign
0.74
D
LIST_S2
Benign
0.70
T;T
M_CAP
Uncertain
0.16
D
MetaRNN
Benign
0.21
T;T
MetaSVM
Benign
-0.59
T
MutationAssessor
Benign
0.34
N;.
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-0.12
N;N
REVEL
Uncertain
0.49
Sift
Uncertain
0.012
D;D
Sift4G
Benign
0.082
T;T
Polyphen
0.0080
B;B
Vest4
0.34
MutPred
0.14
Gain of phosphorylation at P430 (P = 0.0328);.;
MVP
0.98
ClinPred
0.056
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8
Varity_R
0.072
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs267608622; hg19: chrX-153295991; API