NM_000170.3(GLDC):c.2053-5C>G AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(3);Uncertain significance(1) (Last evaluated: Apr 1, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000223973.11

Allele description [Variation Report for NM_000170.3(GLDC):c.2053-5C>G]

NM_000170.3(GLDC):c.2053-5C>G

Gene:
GLDC:glycine decarboxylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p24.1
Genomic location:
Preferred name:
NM_000170.3(GLDC):c.2053-5C>G
HGVS:
  • NC_000009.12:g.6556307G>C
  • NG_016397.1:g.94386C>G
  • NM_000170.2:c.2053-5C>G
  • NM_000170.3:c.2053-5C>GMANE SELECT
  • LRG_643t1:c.2053-5C>G
  • LRG_643:g.94386C>G
  • NC_000009.11:g.6556307G>C
Links:
dbSNP: rs140877566
NCBI 1000 Genomes Browser:
rs140877566
Molecular consequence:
  • NM_000170.2:c.2053-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000170.3:c.2053-5C>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
3

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000281240Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Uncertain Significance
(Mar 22, 2016)
germlineclinical testing

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

SCV001155601CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Likely benign
(Apr 1, 2021)
germlineclinical testing

Citation Link,

SCV001475874Athena Diagnostics Inccriteria provided, single submitter
Likely benign
(Apr 3, 2020)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001795794GeneDxcriteria provided, single submitter
Likely benign
(Aug 21, 2020)
germlineclinical testing

Citation Link,

SCV001966042Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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

Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease.

Bravo-Alonso I, Navarrete R, Arribas-Carreira L, Perona A, Abia D, Couce ML, García-Cazorla A, Morais A, Domingo R, Ramos MA, Swanson MA, Van Hove JLK, Ugarte M, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P.

Hum Mutat. 2017 Jun;38(6):678-691. doi: 10.1002/humu.23208. Epub 2017 Mar 20.

PubMed [citation]
PMID:
28244183
See all PubMed Citations (3)

Details of each submission

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000281240.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Converted during submission to Uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.003251not providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001155601.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From Athena Diagnostics Inc, SCV001475874.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001795794.1

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

Description

This variant is associated with the following publications: (PMID: 28244183)

#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, SCV001966042.1

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

Last Updated: Nov 6, 2021

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