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NM_001110792.2(MECP2):c.397G>C (p.Asp133His) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 18, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004421695.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.397G>C (p.Asp133His)]

NM_001110792.2(MECP2):c.397G>C (p.Asp133His)

Gene:
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.397G>C (p.Asp133His)
HGVS:
  • NC_000023.11:g.154032223C>G
  • NG_007107.3:g.109881G>C
  • NM_001110792.2:c.397G>CMANE SELECT
  • NM_001316337.2:c.82G>C
  • NM_001369391.2:c.82G>C
  • NM_001369392.2:c.82G>C
  • NM_001369393.2:c.82G>C
  • NM_001369394.2:c.82G>C
  • NM_001386137.1:c.-200G>C
  • NM_001386138.1:c.-200G>C
  • NM_001386139.1:c.-200G>C
  • NM_004992.4:c.361G>C
  • NP_001104262.1:p.Asp133His
  • NP_001303266.1:p.Asp28His
  • NP_001356320.1:p.Asp28His
  • NP_001356321.1:p.Asp28His
  • NP_001356322.1:p.Asp28His
  • NP_001356323.1:p.Asp28His
  • NP_004983.1:p.Asp121His
  • LRG_764t1:c.397G>C
  • LRG_764t2:c.361G>C
  • LRG_764:g.109881G>C
  • LRG_764p1:p.Asp133His
  • LRG_764p2:p.Asp121His
  • NC_000023.10:g.153297674C>G
  • NM_004992.3:c.361G>C
Protein change:
D121H
Molecular consequence:
  • NM_001386137.1:c.-200G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-200G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-200G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.397G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.82G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.82G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.82G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.82G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.82G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.361G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004903859Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Oct 18, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genomic mosaicism in the pathogenesis and inheritance of a Rett syndrome cohort.

Zhang Q, Yang X, Wang J, Li J, Wu Q, Wen Y, Zhao Y, Zhang X, Yao H, Wu X, Yu S, Wei L, Bao X.

Genet Med. 2019 Jun;21(6):1330-1338. doi: 10.1038/s41436-018-0348-2. Epub 2018 Nov 8. Erratum in: Genet Med. 2019 Sep;21(9):2162. doi: 10.1038/s41436-019-0461-x.

PubMed [citation]
PMID:
30405208
PMCID:
PMC6752670

Details of each submission

From Ambry Genetics, SCV004903859.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.361G>C (p.D121H) alteration is located in exon 3 (coding exon 2) of the MECP2 gene. This alteration results from a G to C substitution at nucleotide position 361, causing the aspartic acid (D) at amino acid position 121 to be replaced by a histidine (H). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Other alterations at the same codon, c.361G>A (p.D121N), c.362A>T (p.D121V), c.363T>G (p.D121E), and c.362A>G (p.D121G), have been reported in affected individuals (Zhang, 2019). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024