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NM_139058.3(ARX):c.306GGC[17] (p.Ala109_Ala115dup) AND Developmental and epileptic encephalopathy, 1

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
May 22, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000011936.31

Allele description [Variation Report for NM_139058.3(ARX):c.306GGC[17] (p.Ala109_Ala115dup)]

NM_139058.3(ARX):c.306GGC[17] (p.Ala109_Ala115dup)

Genes:
LOC109610631:aristaless related homeobox polyalanine expansion region [Gene]
ARX:aristaless related homeobox [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xp21.3
Genomic location:
Preferred name:
NM_139058.3(ARX):c.306GGC[17] (p.Ala109_Ala115dup)
Other names:
NP_620689.1:p.(Ala109_Ala115dup)
HGVS:
  • NC_000023.11:g.25013662CGC[17]
  • NG_008281.1:g.7260GGC[17]
  • NG_052655.1:g.233CGC[17]
  • NM_139058.3:c.306GGC[17]MANE SELECT
  • NP_620689.1:p.Ala109_Ala115dup
  • NC_000023.10:g.25031776_25031777insGCCGCCGCCGCCGCCGCCGCC
  • NC_000023.10:g.25031779CGC[17]
  • NM_139058.2:c.315_335dupGGCGGCGGCGGCGGCGGCGGC
  • NM_139058.3:c.315_335dupMANE SELECT
Links:
OMIM: 300382.0001; dbSNP: rs387906492
NCBI 1000 Genomes Browser:
rs387906492
Molecular consequence:
  • NM_139058.3:c.306GGC[17] - inframe_insertion - [Sequence Ontology: SO:0001821]
Observations:
1

Condition(s)

Name:
Developmental and epileptic encephalopathy, 1 (DEE1)
Synonyms:
INFANTILE SPASM SYNDROME, X-LINKED 1; X-linked infantile spasms; West's syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010632; MedGen: C3463992; OMIM: 308350

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000032169OMIM
no assertion criteria provided
Pathogenic
(Jul 31, 2007)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV001426447Centogene AG - the Rare Disease Company
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicde novoclinical testing

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

SCV0025209843billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 22, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedde novoyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy.

Strømme P, Mangelsdorf ME, Shaw MA, Lower KM, Lewis SM, Bruyere H, Lütcherath V, Gedeon AK, Wallace RH, Scheffer IE, Turner G, Partington M, Frints SG, Fryns JP, Sutherland GR, Mulley JC, Gécz J.

Nat Genet. 2002 Apr;30(4):441-5. Epub 2002 Mar 11.

PubMed [citation]
PMID:
11889467

Confirmation of linkage in X-linked infantile spasms (West syndrome) and refinement of the disease locus to Xp21.3-Xp22.1.

Bruyere H, Lewis S, Wood S, MacLeod PJ, Langlois S.

Clin Genet. 1999 Mar;55(3):173-81.

PubMed [citation]
PMID:
10334471
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000032169.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

In 2 unrelated families, 1 Canadian and 2 Belgian, with developmental and epileptic encephalopathy (DEE1; 308350), described as infantile spasm syndrome, Stromme et al. (2002) found that 8 and 2 male affected members, respectively, had an additional stretch of 7 tandem GCG repeats within the normal stretch of 10 GCG triplet repeats in exon 2. These families had been described by Bruyere et al. (1999) and Claes et al. (1997). The effect of the mutation on the protein product was polyalanine expansion. The haplotype background of the mutation was different in the 2 families, indicating that a recurrent mutation had occurred. The normal tract of 16 alanine residues (amino acids 100-115) was expanded to 23.

Shoubridge et al. (2007) showed that this polyalanine expansion mutation was associated with an increased propensity of ARX protein aggregation and a shift from nuclear to cytoplasmic localization.

Guerrini et al. (2007) identified the (GCG)10+7 expansion in 6 boys, including 2 pairs of brothers, with a severe form of DEE1, which they termed infantile epileptic-dyskinetic encephalopathy, including chorea and dystonia. All 6 boys also had severe mental retardation. Seizure onset occurred between 2 and 5 months of age and earlier than dystonia, which was severe and progressed to quadriplegic dyskinesia. Three children had recurrent, life-threatening status dystonicus. Brain MRI showed basal ganglia abnormalities in 4 patients.

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

From Centogene AG - the Rare Disease Company, SCV001426447.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002520984.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This variant has been reported as pathogenic more than twice (ClinVar ID: VCV000011186), along with assertion criteria based on the ACMG guidelines. It is absent from the gnomAD v2.1.1 dataset. Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Nov 10, 2024