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NM_000481.4(AMT):c.14dup (p.Ser6fs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000730238.6

Allele description

NM_000481.4(AMT):c.14dup (p.Ser6fs)

Genes:
AMT:aminomethyltransferase [Gene - OMIM - HGNC]
NICN1:nicolin 1, tubulin polyglutamylase complex subunit [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_000481.4(AMT):c.14dup (p.Ser6fs)
HGVS:
  • NC_000003.12:g.49422437dup
  • NG_015986.1:g.5242dup
  • NG_033046.1:g.11888dup
  • NM_000481.3:c.14dupT
  • NM_000481.4:c.14dupMANE SELECT
  • NM_001164710.2:c.14dup
  • NM_001164711.2:c.14dup
  • NM_001164712.2:c.14dup
  • NM_032316.3:c.*2396dupMANE SELECT
  • NP_000472.2:p.Ser6fs
  • NP_001158182.1:p.Ser6fs
  • NP_001158183.1:p.Ser6fs
  • NP_001158184.1:p.Ser6fs
  • LRG_537t1:c.14dup
  • LRG_537:g.5242dup
  • NC_000003.11:g.49459869_49459870insA
  • NC_000003.11:g.49459870dup
  • NM_000481.4:c.14dup
  • NR_028435.2:n.37dup
Protein change:
S6fs
Links:
dbSNP: rs773988915
NCBI 1000 Genomes Browser:
rs773988915
Molecular consequence:
  • NM_032316.3:c.*2396dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000481.4:c.14dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164710.2:c.14dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164711.2:c.14dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164712.2:c.14dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_028435.2:n.37dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
3

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
SCV000857963Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(Nov 9, 2017)
germlineclinical testing

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

Citation Link,

SCV004703313CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Jan 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT.

Coughlin CR 2nd, Swanson MA, Kronquist K, Acquaviva C, Hutchin T, Rodríguez-Pombo P, Väisänen ML, Spector E, Creadon-Swindell G, Brás-Goldberg AM, Rahikkala E, Moilanen JS, Mahieu V, Matthijs G, Bravo-Alonso I, Pérez-Cerdá C, Ugarte M, Vianey-Saban C, Scharer GH, Van Hove JL.

Genet Med. 2017 Jan;19(1):104-111. doi: 10.1038/gim.2016.74. Epub 2016 Jun 30. Erratum in: Genet Med. 2018 Jan 04;:.

PubMed [citation]
PMID:
27362913

Details of each submission

From Eurofins Ntd Llc (ga), SCV000857963.1

#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 CeGaT Center for Human Genetics Tuebingen, SCV004703313.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided

Description

AMT: PVS1, PM2, PM3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Apr 15, 2024