NM_004247.4(EFTUD2):c.2624del (p.Ile875fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 31, 2022
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:: RCV002255045.3

Allele description [Variation Report for NM_004247.4(EFTUD2):c.2624del (p.Ile875fs)]

NM_004247.4(EFTUD2):c.2624del (p.Ile875fs)

Gene:

EFTUD2:elongation factor Tu GTP binding domain containing 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_004247.4(EFTUD2):c.2624del (p.Ile875fs)

HGVS:

NC_000017.11:g.44852500del
NG_032674.1:g.52126del
NM_001142605.2:c.2519del
NM_001258353.2:c.2624del
NM_001258354.2:c.2594del
NM_004247.4:c.2624delMANE SELECT
NP_001136077.1:p.Ile840fs
NP_001245282.1:p.Ile875fs
NP_001245283.1:p.Ile865fs
NP_004238.3:p.Ile875fs
NC_000017.10:g.42929868del
NM_004247.3:c.2624del

Protein change:

I840fs

Links:

dbSNP: rs2145431524

NCBI 1000 Genomes Browser:

rs2145431524

Molecular consequence:

NM_001142605.2:c.2519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258353.2:c.2624del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258354.2:c.2594del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004247.4:c.2624del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002526298	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (May 31, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002526298

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(May 31, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV002526298.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 98 amino acids are lost and replaced with 59 incorrect amino acids; Not observed in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Dec 24, 2023

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Relating variation to medicine