NM_003359.4(UGDH):c.1136A>T (p.Asp379Val) AND Developmental and epileptic encephalopathy, 84

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 20, 2023
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:: RCV004771695.1

Allele description [Variation Report for NM_003359.4(UGDH):c.1136A>T (p.Asp379Val)]

NM_003359.4(UGDH):c.1136A>T (p.Asp379Val)

Gene:

UGDH:UDP-glucose 6-dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p14

Genomic location:

Preferred name:

NM_003359.4(UGDH):c.1136A>T (p.Asp379Val)

HGVS:

NC_000004.12:g.39505272T>A
NM_001184700.2:c.935A>T
NM_001184701.2:c.845A>T
NM_003359.4:c.1136A>TMANE SELECT
NP_001171629.1:p.Asp312Val
NP_001171630.1:p.Asp282Val
NP_003350.1:p.Asp379Val
NC_000004.11:g.39506892T>A

Protein change:

D282V

Molecular consequence:

NM_001184700.2:c.935A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001184701.2:c.845A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003359.4:c.1136A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 84
Synonyms:: EPILEPTIC ENCEPHALOPATHY, EARLY IFANTILE, 84
Identifiers:: MONDO: MONDO:0032918; MedGen: C5394081; OMIM: 618792

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005382377	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 20, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005382377

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 20, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV005382377.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The missense c.1136A>T (p.Asp379Val) variant in the UGDH gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is absent in the gnomAD Exomes. The amino acid Aspartic acid at position 379 is changed to a Valine changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen - Probably damaging, SIFT – Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. The amino acid Aspartic acid in UGDH is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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