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NM_001110792.2(MECP2):c.641C>T (p.Ala214Val) AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 30, 2021
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:
RCV003227673.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.641C>T (p.Ala214Val)]

NM_001110792.2(MECP2):c.641C>T (p.Ala214Val)

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.641C>T (p.Ala214Val)
Other names:
p.A202V:GCC>GTC
HGVS:
  • NC_000023.11:g.154031223G>A
  • NG_007107.3:g.110881C>T
  • NM_001110792.2:c.641C>TMANE SELECT
  • NM_001316337.2:c.326C>T
  • NM_001369391.2:c.326C>T
  • NM_001369392.2:c.326C>T
  • NM_001369393.2:c.326C>T
  • NM_001369394.2:c.326C>T
  • NM_001386137.1:c.-65C>T
  • NM_001386138.1:c.-65C>T
  • NM_001386139.1:c.-65C>T
  • NM_004992.4:c.605C>T
  • NP_001104262.1:p.Ala214Val
  • NP_001303266.1:p.Ala109Val
  • NP_001356320.1:p.Ala109Val
  • NP_001356321.1:p.Ala109Val
  • NP_001356322.1:p.Ala109Val
  • NP_001356323.1:p.Ala109Val
  • NP_004983.1:p.Ala202Val
  • NP_004983.1:p.Ala202Val
  • LRG_764t1:c.641C>T
  • LRG_764t2:c.605C>T
  • LRG_764:g.110881C>T
  • LRG_764p1:p.Ala214Val
  • LRG_764p2:p.Ala202Val
  • NC_000023.10:g.153296674G>A
  • NG_007107.2:g.110905C>T
  • NM_004992.3:c.605C>T
Protein change:
A109V
Links:
dbSNP: rs587783138
NCBI 1000 Genomes Browser:
rs587783138
Molecular consequence:
  • NM_001386137.1:c.-65C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-65C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-65C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Severe neonatal-onset encephalopathy with microcephaly
Synonyms:
Encephalopathy, neonatal severe; Encephalopathy, neonatal severe, due to MECP2 mutations
Identifiers:
MONDO: MONDO:0010397; MedGen: C1968556; Orphanet: 209370; OMIM: 300673
Name:
Syndromic X-linked intellectual disability Lubs type (MRXSL)
Synonyms:
MENTAL RETARDATION, X-LINKED, WITH RECURRENT RESPIRATORY INFECTIONS; Lubs X-linked mental retardation syndrome; XLMR syndrome, Lubs type; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010283; MedGen: C1846058; OMIM: 300260
Name:
X-linked intellectual disability-psychosis-macroorchidism syndrome (MRXS13)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC 13; PPM-X syndrome
Identifiers:
MONDO: MONDO:0010235; MedGen: C0796222; Orphanet: 3077; OMIM: 300055
Name:
Rett syndrome (RTT)
Synonyms:
Autism, dementia, ataxia, and loss of purposeful hand use; Rett's disorder
Identifiers:
MONDO: MONDO:0010726; MedGen: C0035372; Orphanet: 3095; Orphanet: 778; OMIM: 312750
Name:
Autism, susceptibility to, X-linked 3 (AUTSX3)
Synonyms:
Austism susceptibility, X-linked; Autism susceptibility, X-linked 3
Identifiers:
MONDO: MONDO:0010342; MedGen: C1845336; OMIM: 300496

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003924123Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Mar 30, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003924123.1

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

Description

MECP2 NM_004992.3 exon 4 p.Ala202Val (c.605C>T): This variant has not been reported in the literature but is present in 0.02% (5/19080) of South Asian alleles including 3 hemizygotes in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/X-153296674-G-A?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:156668). This variant amino acid Valine (Val) is present in multiple species and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Nov 10, 2024