rs907041830
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP5_Moderate
The NM_003907.3(EIF2B5):c.1010A>G(p.His337Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 31)
Consequence
EIF2B5
NM_003907.3 missense
NM_003907.3 missense
Scores
1
11
6
Clinical Significance
Conservation
PhyloP100: 8.89
Genes affected
EIF2B5 (HGNC:3261): (eukaryotic translation initiation factor 2B subunit epsilon) This gene encodes one of five subunits of eukaryotic translation initiation factor 2B (EIF2B), a GTP exchange factor for eukaryotic initiation factor 2 and an essential regulator for protein synthesis. Mutations in this gene and the genes encoding other EIF2B subunits have been associated with leukoencephalopathy with vanishing white matter. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
?
In a strand (size 2) in uniprot entity EI2BE_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_003907.3
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 3-184140584-A-G is Pathogenic according to our data. Variant chr3-184140584-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 590971.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2B5 | NM_003907.3 | c.1010A>G | p.His337Arg | missense_variant | 7/16 | ENST00000648915.2 | |
EIF2B5 | XM_047449148.1 | c.1010A>G | p.His337Arg | missense_variant | 7/11 | ||
EIF2B5 | XM_011513265.1 | c.260A>G | p.His87Arg | missense_variant | 3/12 | ||
EIF2B5 | XM_011513266.4 | c.173A>G | p.His58Arg | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2B5 | ENST00000648915.2 | c.1010A>G | p.His337Arg | missense_variant | 7/16 | NM_003907.3 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Vanishing white matter disease Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia | Oct 29, 2018 | The variant identified not been previously reported in public databases. This variant was identified in a patient diagnosed with Vanishing white matter leukodystrophy, a disease characterized by variable neurologic features, including progressive cerebellar ataxia, spasticity, and cognitive impairment associated with white matter lesions on brain imaging. We consider that these variants in compound heterozygosis are probably pathogenic because they are in a critical region and coding for the EIF2B5 gene; The gene has previously been associated with this disease as reported in the OMIM database and PubMed (Sharma et al., 2015; Woody et al., 2015). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;.
REVEL
Uncertain
Sift
Benign
T;.;.
Sift4G
Benign
T;.;.
Polyphen
P;.;P
Vest4
MutPred
Gain of sheet (P = 0.0477);.;Gain of sheet (P = 0.0477);
MVP
MPC
ClinPred
D
GERP RS
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