8-143580550-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001130053.5(EEF1D):​c.1666C>A​(p.Pro556Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)

Consequence

EEF1D
NM_001130053.5 missense

Scores

5
10
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.88
Variant links:
Genes affected
EEF1D (HGNC:3211): (eukaryotic translation elongation factor 1 delta) This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.764

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EEF1DNM_001130053.5 linkc.1666C>A p.Pro556Thr missense_variant Exon 8 of 10 ENST00000618139.4 NP_001123525.3 P29692-2D3DWK1B2RAR6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EEF1DENST00000618139.4 linkc.1666C>A p.Pro556Thr missense_variant Exon 8 of 10 5 NM_001130053.5 ENSP00000484536.2 P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
250942
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135698
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000883
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
34
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.43
BayesDel_addAF
Pathogenic
0.35
D
BayesDel_noAF
Pathogenic
0.26
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.14
T;T;.;T;T;.;.;.;T;T;.;.;.;T;.;T;T;T
Eigen
Uncertain
0.65
Eigen_PC
Uncertain
0.59
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.96
D;.;D;D;D;D;.;.;.;.;D;D;D;D;D;.;D;D
M_CAP
Benign
0.047
D
MetaRNN
Pathogenic
0.76
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.023
T
MutationAssessor
Pathogenic
2.9
M;M;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.52
T
PROVEAN
Pathogenic
-7.2
D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;D;D;D
REVEL
Uncertain
0.46
Sift
Benign
0.032
D;D;D;T;D;D;D;D;D;D;D;D;.;D;D;D;D;D
Sift4G
Uncertain
0.036
D;D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;D;.
Polyphen
0.99
D;D;D;.;D;.;D;.;D;D;.;.;.;.;.;.;.;.
Vest4
0.72
MutPred
0.29
.;.;.;.;Gain of phosphorylation at P606 (P = 0.032);.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.86
MPC
0.25
ClinPred
0.99
D
GERP RS
4.6
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.56
gMVP
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs369674762; hg19: chr8-144662720; API