NM_000481.4(AMT):c.631G>A (p.Glu211Lys) AND Non-ketotic hyperglycinemia

Clinical significance:Benign/Likely benign (Last evaluated: Jul 10, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
7 submissions [Details]
Record status:
current
Accession:
RCV000549987.9

Allele description [Variation Report for NM_000481.4(AMT):c.631G>A (p.Glu211Lys)]

NM_000481.4(AMT):c.631G>A (p.Glu211Lys)

Gene:
AMT:aminomethyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_000481.4(AMT):c.631G>A (p.Glu211Lys)
HGVS:
  • NC_000003.12:g.49419325C>T
  • NG_015986.1:g.8354G>A
  • NM_000481.3:c.631G>A
  • NM_000481.4:c.631G>AMANE SELECT
  • NM_001164710.2:c.499G>A
  • NM_001164711.2:c.463G>A
  • NM_001164712.2:c.631G>A
  • NP_000472.2:p.Glu211Lys
  • NP_000472.2:p.Glu211Lys
  • NP_001158182.1:p.Glu167Lys
  • NP_001158183.1:p.Glu155Lys
  • NP_001158184.1:p.Glu211Lys
  • LRG_537t1:c.631G>A
  • LRG_537:g.8354G>A
  • LRG_537p1:p.Glu211Lys
  • NC_000003.11:g.49456758C>T
  • NR_028435.2:n.640G>A
Protein change:
E155K
Links:
dbSNP: rs116192290
NCBI 1000 Genomes Browser:
rs116192290
Molecular consequence:
  • NM_000481.3:c.631G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000481.4:c.631G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164710.2:c.499G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164711.2:c.463G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164712.2:c.631G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_028435.2:n.640G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Non-ketotic hyperglycinemia (GCE)
Synonyms:
Glycine encephalopathy; Nonketotic hyperglycinemia
Identifiers:
MONDO: MONDO:0011612; MedGen: C0751748; Orphanet: 407; OMIM: 605899; Human Phenotype Ontology: HP:0008288

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000636427Invitaecriteria provided, single submitter
Benign
(Dec 8, 2020)
germlineclinical testing

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

SCV000734285Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensusno assertion criteria providedBenigngermlineclinical testing

SCV000743157Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Oct 9, 2014)
germlineclinical testing

Citation Link,

SCV001136523Mendelicscriteria provided, single submitter
Likely benign
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001311639Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

Citation Link,

SCV001456314Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

SCV001762853Nilou-Genome Labcriteria provided, single submitter
Likely benign
(Jul 10, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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, SCV000636427.3

#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, SCV000734285.1

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743157.1

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

From Mendelics, SCV001136523.1

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

From Illumina Clinical Services Laboratory,Illumina, SCV001311639.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

From Natera, Inc., SCV001456314.1

#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, SCV001762853.1

#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: Nov 27, 2021

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