NM_000159.4(GCDH):c.1143C>T (p.Ile381=) AND Glutaric aciduria, type 1

Clinical significance:Likely benign (Last evaluated: May 18, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000525178.7

Allele description [Variation Report for NM_000159.4(GCDH):c.1143C>T (p.Ile381=)]

NM_000159.4(GCDH):c.1143C>T (p.Ile381=)

Gene:
GCDH:glutaryl-CoA dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_000159.4(GCDH):c.1143C>T (p.Ile381=)
HGVS:
  • NC_000019.10:g.12897763C>T
  • NG_009292.1:g.11604C>T
  • NG_033049.1:g.26510G>A
  • NM_000159.4:c.1143C>TMANE SELECT
  • NM_013976.4:c.1143C>T
  • NP_000150.1:p.Ile381=
  • NP_039663.1:p.Ile381=
  • NC_000019.9:g.13008577C>T
  • NM_000159.2:c.1143C>T
  • NM_000159.3:c.1143C>T
  • NR_102316.1:n.1306C>T
  • NR_102317.1:n.1524C>T
Links:
dbSNP: rs142553521
NCBI 1000 Genomes Browser:
rs142553521
Molecular consequence:
  • NR_102316.1:n.1306C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_102317.1:n.1524C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000159.4:c.1143C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_013976.4:c.1143C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Glutaric aciduria, type 1 (GA1)
Synonyms:
GA I; Glutaryl-CoA dehydrogenase deficiency; Glutaric acidemia type I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009281; MedGen: C0268595; Orphanet: 25; OMIM: 231670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000631930Invitaecriteria provided, single submitter
Likely benign
(Dec 8, 2020)
germlineclinical testing

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

SCV000733850Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

SCV000745269Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Jun 28, 2017)
germlineclinical testing

Citation Link,

SCV001460071Natera, Inc.no assertion criteria providedLikely benign
(Nov 11, 2019)
germlineclinical testing

SCV001653487Nilou-Genome Labcriteria provided, single submitter
Likely benign
(May 18, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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 Invitae, SCV000631930.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733850.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745269.1

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

From Natera, Inc., SCV001460071.1

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

From Nilou-Genome Lab, SCV001653487.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 7, 2021

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