NM_001958.5(EEF1A2):c.208G>A (p.Gly70Ser) AND Intellectual disability, autosomal dominant 38

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 2, 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:: RCV001775080.3

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]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal dominant 38 (MRD38)
Synonyms:: PSYCHOMOTOR RETARDATION, EPILEPSY, AND LANGUAGE DISABILITY SYNDROME; INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 38
Identifiers:: MONDO: MONDO:0014617; MedGen: C4225343; OMIM: 616393

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002012021	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 2, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23033978, 23647072, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002012021

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 2, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing

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 (3)

Details of each submission

From 3billion, SCV002012021.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (3)

Description

Same nucleotide change resulting in same amino acid change has been previously reported at least twice as de novoo in similarly affected indivisual (PMID: 23033978,23647072, PS2, PS4_M). The missense variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PM1). It is not observed in the gnomAD v2.1.1 dataset (PM2). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.919, 3Cnet: 0.730, PP3). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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