NM_002225.5(IVD):c.466G>A (p.Gly156Ser) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 7, 2017
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:: RCV000497808.2

Allele description [Variation Report for NM_002225.5(IVD):c.466G>A (p.Gly156Ser)]

NM_002225.5(IVD):c.466G>A (p.Gly156Ser)

Gene:

IVD:isovaleryl-CoA dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_002225.5(IVD):c.466G>A (p.Gly156Ser)

HGVS:

NC_000015.10:g.40411269G>A
NG_011986.2:g.10785G>A
NM_001159508.3:c.376G>A
NM_001354597.3:c.418G>A
NM_001354598.3:c.466G>A
NM_001354599.3:c.553G>A
NM_001354600.3:c.553G>A
NM_001354601.3:c.466G>A
NM_002225.5:c.466G>AMANE SELECT
NP_001152980.2:p.Gly126Ser
NP_001341526.1:p.Gly140Ser
NP_001341527.2:p.Gly156Ser
NP_001341528.2:p.Gly185Ser
NP_001341529.2:p.Gly185Ser
NP_001341530.2:p.Gly156Ser
NP_002216.3:p.Gly156Ser
NC_000015.9:g.40703468G>A
NM_002225.3:c.475G>A
NR_148925.2:n.878G>A

Protein change:

G126S

Links:

dbSNP: rs1555404010

NCBI 1000 Genomes Browser:

rs1555404010

Molecular consequence:

NM_001159508.3:c.376G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354597.3:c.418G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354598.3:c.466G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354599.3:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354600.3:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354601.3:c.466G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002225.5:c.466G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148925.2:n.878G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000589861	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Aug 7, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000589861

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Aug 7, 2017)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000589861.2

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

Description

The G159S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G159S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Another missense variant in the same residue (G159A) has been reported in the Human Gene Mutation Database in association with isovaleric acidemia (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

#	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: Mar 16, 2024

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