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NM_001958.5(EEF1A2):c.208G>A (p.Gly70Ser) AND Developmental and epileptic encephalopathy, 33

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 8, 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:
RCV000087144.15

Allele description [Variation Report for NM_001958.5(EEF1A2):c.208G>A (p.Gly70Ser)]

NM_001958.5(EEF1A2):c.208G>A (p.Gly70Ser)

Gene:
EEF1A2:eukaryotic translation elongation factor 1 alpha 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.33
Genomic location:
Preferred name:
NM_001958.5(EEF1A2):c.208G>A (p.Gly70Ser)
HGVS:
  • NC_000020.11:g.63495972C>T
  • NG_034083.1:g.8344G>A
  • NM_001958.5:c.208G>AMANE SELECT
  • NP_001949.1:p.Gly70Ser
  • NP_001949.1:p.Gly70Ser
  • NC_000020.10:g.62127325C>T
  • NM_001958.2:c.208G>A
  • NM_001958.3:c.208G>A
  • NM_001958.4:c.208G>A
  • Q05639:p.Gly70Ser
Protein change:
G70S; GLY70SER
Links:
UniProtKB: Q05639#VAR_069395; OMIM: 602959.0001; dbSNP: rs587777162
NCBI 1000 Genomes Browser:
rs587777162
Molecular consequence:
  • NM_001958.5:c.208G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 33 (DEE33)
Synonyms:
Epileptic encephalopathy, early infantile, 33
Identifiers:
MONDO: MONDO:0014625; MedGen: C4225337; Orphanet: 442835; OMIM: 616409

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000120006OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2013)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000962952Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Oct 8, 2023)
germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Diagnostic exome sequencing in persons with severe intellectual disability.

de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE.

N Engl J Med. 2012 Nov 15;367(20):1921-9. doi: 10.1056/NEJMoa1206524. Epub 2012 Oct 3.

PubMed [citation]
PMID:
23033978

Exome sequencing reveals new causal mutations in children with epileptic encephalopathies.

Veeramah KR, Johnstone L, Karafet TM, Wolf D, Sprissler R, Salogiannis J, Barth-Maron A, Greenberg ME, Stuhlmann T, Weinert S, Jentsch TJ, Pazzi M, Restifo LL, Talwar D, Erickson RP, Hammer MF.

Epilepsia. 2013 Jul;54(7):1270-81. doi: 10.1111/epi.12201. Epub 2013 May 3.

PubMed [citation]
PMID:
23647072
PMCID:
PMC3700577
See all PubMed Citations (9)

Details of each submission

From OMIM, SCV000120006.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In a 22-year-old woman (trio 91) with developmental and epileptic encephalopathy-33 (DEE33; 616409), de Ligt et al. (2012) identified a de novo heterozygous c.208G-A transition in the EEF1A2 gene, resulting in a gly70-to-ser (G70S) substitution at a highly conserved residue. The patient had neonatal hypotonia and developed seizures at age 4 months. She had severely delayed psychomotor development, with limited speech, autistic features, and aggressive behavior. The patient was ascertained from a larger cohort of 100 patients with severe intellectual disability who underwent exome sequencing. Functional studies of the variant were not performed.

Veeramah et al. (2013) identified a de novo heterozygous G70S substitution in a 14-year-old boy with DEE33. He developed refractory seizures with hypsarrhythmia at age 10 weeks, and later showed severe developmental delay, with episodic regression, acquired microcephaly, hypotonia, incoordination, and gait instability. He was nonverbal. The phenotype was consistent with a clinical diagnosis of West syndrome. The mutation, which was found by whole-exome sequencing, was not present in the 1000 Genomes Project or Exome Sequencing Project databases. The patient was 1 of 10 probands with epileptic encephalopathy who underwent whole-exome sequencing. Functional studies of the variant were not performed.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000962952.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 70 of the EEF1A2 protein (p.Gly70Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with epileptic encephalopathy (PMID: 23033978, 23647072, 26795593, 27441201, 27652284, 28628100). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 100782). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt EEF1A2 protein function. Experimental studies have shown that this missense change affects EEF1A2 function (PMID: 28378778, 28911200). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 20, 2024