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NM_020365.5(EIF2B3):c.89T>C (p.Val30Ala)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Jul 13, 2020)
Last evaluated:
Jun 4, 2020
Accession:
VCV000617677.2
Variation ID:
617677
Description:
single nucleotide variant
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NM_020365.5(EIF2B3):c.89T>C (p.Val30Ala)

Allele ID
609080
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.1
Genomic location
1: 44981080 (GRCh38) GRCh38 UCSC
1: 45446752 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.44981080A>G
NC_000001.10:g.45446752A>G
NM_020365.5:c.89T>C MANE Select NP_065098.1:p.Val30Ala missense
... more HGVS
Protein change
V30A
Other names
-
Canonical SPDI
NC_000001.11:44981079:A:G
Functional consequence
Decreased function
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
dbSNP: rs752636698
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, single submitter Jun 4, 2020 RCV000754838.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EIF2B3 - - GRCh38
GRCh37
73 89

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 04, 2020)
criteria provided, single submitter
Method: clinical testing
Leukoencephalopathy with vanishing white matter
(Autosomal recessive inheritance)
Allele origin: inherited
Department of Laboratory Medicine,Yonsei University College of Medicine
Accession: SCV001364278.1
Submitted: (Jul 13, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The c.89T>C variant has been identified in 0.0007953% by the Genome Aggregation Database (gnomAD, rs752636698). This variant has been reported in the compound heterozygous state … (more)
Uncertain significance
(Oct 10, 2017)
no assertion criteria provided
Method: research
Leukoencephalopathy with vanishing white matter
(Autosomal recessive inheritance)
Allele origin: paternal
Department of Rehabilitation Medicine, Incheon St. Mary’s Hospital,College of Medicine, The Catholic University of Korea
Accession: SCV000882594.1
Submitted: (Feb 06, 2019)
Evidence details

Functional evidence

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Functional consequence Method Result Submitter Supporting information
Decreased function
Department of Laboratory Medicine,Yonsei University College of Medicine
Accession: SCV001364278.1
Submitted: (Jul 13, 2020)
Evidence details
Publications
PubMed (1)

Citations for this variant

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Title Author Journal Year Link
Correlation Between Vanishing White Matter Disease and Novel Heterozygous EIF2B3 Variants Using Next-Generation Sequencing: A Case Report. Hyun SE Annals of rehabilitation medicine 2019 PMID: 31072091

Text-mined citations for rs752636698...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 08, 2021