U.S. flag

An official website of the United States government

NM_004247.4(EFTUD2):c.105+2T>G AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 11, 2019
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:
RCV001266947.4

Allele description [Variation Report for NM_004247.4(EFTUD2):c.105+2T>G]

NM_004247.4(EFTUD2):c.105+2T>G

Gene:
EFTUD2:elongation factor Tu GTP binding domain containing 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_004247.4(EFTUD2):c.105+2T>G
HGVS:
  • NC_000017.11:g.44894415A>C
  • NG_032674.1:g.10211T>G
  • NM_001142605.2:c.-1+4954T>G
  • NM_001258353.2:c.105+2T>G
  • NM_001258354.2:c.105+2T>G
  • NM_004247.4:c.105+2T>GMANE SELECT
  • NC_000017.10:g.42971783A>C
  • NM_004247.3:c.105+2T>G
Links:
dbSNP: rs2051339634
NCBI 1000 Genomes Browser:
rs2051339634
Molecular consequence:
  • NM_001142605.2:c.-1+4954T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258353.2:c.105+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258354.2:c.105+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004247.4:c.105+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001445128Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Mar 11, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV001445128.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The alteration is predicted to abolish the native donor splice site: _x000D_ _x000D_ The c.105+2T>G alteration is in intron 2 of the EFTUD2 gene and results from a T to G substitution at nucleotide position 105+2. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (Richards, 2015). The alteration is not observed in population databases:_x000D_ _x000D_ Based on data from the Genome Aggregation Database (gnomAD), the EFTUD2 c.105+2T>G alteration was not observed, with coverage at this position. The altered nucleotide is conserved throughout evolution:_x000D_ _x000D_ The c.105+2T nucleotide is conserved in available vertebrate species. The alteration is predicted to affect splicing by in silico models:_x000D_ _x000D_ Based on BDGP and ESEfinder splice site in silico tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Based on the available evidence, this alteration is classified as likely pathogenic.

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

Last Updated: Apr 20, 2024