chr17-44851362-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2PP3
The NM_004247.4(EFTUD2):c.2831G>T(p.Ser944Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
EFTUD2
NM_004247.4 missense
NM_004247.4 missense
Scores
10
6
2
Clinical Significance
Conservation
PhyloP100: 7.47
Genes affected
EFTUD2 (HGNC:30858): (elongation factor Tu GTP binding domain containing 2) This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, EFTUD2
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.817
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFTUD2 | NM_004247.4 | c.2831G>T | p.Ser944Ile | missense_variant | 28/28 | ENST00000426333.7 | |
EFTUD2 | NM_001258353.2 | c.2831G>T | p.Ser944Ile | missense_variant | 28/28 | ||
EFTUD2 | NM_001258354.2 | c.2801G>T | p.Ser934Ile | missense_variant | 28/28 | ||
EFTUD2 | NM_001142605.2 | c.2726G>T | p.Ser909Ile | missense_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFTUD2 | ENST00000426333.7 | c.2831G>T | p.Ser944Ile | missense_variant | 28/28 | 1 | NM_004247.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250114Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135400
GnomAD3 exomes
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461398Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727018
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GnomAD4 genome ? Cov.: 32
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?
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EFTUD2-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 28, 2022 | The EFTUD2 c.2831G>T variant is predicted to result in the amino acid substitution p.Ser944Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00089% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-42928730-C-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;D;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.;.;.;D
REVEL
Uncertain
Sift
Uncertain
D;.;.;.;D
Sift4G
Uncertain
T;T;T;D;D
Polyphen
D;.;D;.;.
Vest4
MutPred
Loss of disorder (P = 0.0081);.;Loss of disorder (P = 0.0081);.;.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at