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NM_000182.5(HADHA):c.2107G>A (p.Gly703Arg) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Mar 1, 2017
Review status:
criteria provided, conflicting classifications
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:
RCV000493353.26

Allele description [Variation Report for NM_000182.5(HADHA):c.2107G>A (p.Gly703Arg)]

NM_000182.5(HADHA):c.2107G>A (p.Gly703Arg)

Genes:
GAREM2:GRB2 associated regulator of MAPK1 subtype 2 [Gene - OMIM - HGNC]
HADHA:hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p23.3
Genomic location:
Preferred name:
NM_000182.5(HADHA):c.2107G>A (p.Gly703Arg)
HGVS:
  • NC_000002.12:g.26191522C>T
  • NG_007121.2:g.58100G>A
  • NM_000182.5:c.2107G>AMANE SELECT
  • NP_000173.2:p.Gly703Arg
  • LRG_747t1:c.2107G>A
  • LRG_747:g.58100G>A
  • LRG_747p1:p.Gly703Arg
  • NC_000002.11:g.26414391C>T
  • NM_000182.4:c.2107G>A
Protein change:
G703R; GLY703ARG
Links:
OMIM: 600890.0012; dbSNP: rs200438844
NCBI 1000 Genomes Browser:
rs200438844
Molecular consequence:
  • NM_000182.5:c.2107G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000582011GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Likely pathogenic
(Jul 22, 2015)
germlineclinical testing

Citation Link,

SCV000608925CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Mar 1, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000582011.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The G703R variant has published previously in a patient who had an abnormal newborn screening result for long chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency who also harbored the E510Q variant (Sykut-Cegielska et al. 2011). The G703R 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. In silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variant in a nearby residue (D701G) has been reported in the Human Gene Mutation Database in association with mitochondrial trifunctional protein (MTP) deficiency (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, the G703R variant was interpreted to be a strong candidate for a pathogenic variant, however the possibility that it is a benign variant cannot be excluded.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV000608925.31

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 3, 2024