NM_000481.4(AMT):c.175G>A (p.Val59Met) AND Non-ketotic hyperglycinemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 2, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003051832.3

Allele description [Variation Report for NM_000481.4(AMT):c.175G>A (p.Val59Met)]

NM_000481.4(AMT):c.175G>A (p.Val59Met)

Gene:

AMT:aminomethyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_000481.4(AMT):c.175G>A (p.Val59Met)

HGVS:

NC_000003.12:g.49422187C>T
NG_015986.1:g.5492G>A
NG_033046.1:g.12138G>A
NG_099407.1:g.940C>T
NG_099408.1:g.187C>T
NM_000481.4:c.175G>AMANE SELECT
NM_001164710.2:c.175G>A
NM_001164711.2:c.90+174G>A
NM_001164712.2:c.175G>A
NP_000472.2:p.Val59Met
NP_000472.2:p.Val59Met
NP_001158182.1:p.Val59Met
NP_001158184.1:p.Val59Met
LRG_537t1:c.175G>A
LRG_537:g.5492G>A
LRG_537p1:p.Val59Met
NC_000003.11:g.49459620C>T
NM_000481.3:c.175G>A
NR_028435.2:n.184G>A

Protein change:

V59M

Molecular consequence:

NM_001164711.2:c.90+174G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000481.4:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164710.2:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164712.2:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_028435.2:n.184G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Non-ketotic hyperglycinemia
Synonyms:: Glycine encephalopathy; Nonketotic hyperglycinemia
Identifiers:: MONDO: MONDO:0011612; MedGen: C0751748; Orphanet: 407; OMIM: PS605899; Human Phenotype Ontology: HP:0008288

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003340131	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 2, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003340131

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 2, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003340131.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 59 of the AMT protein (p.Val59Met). This variant is present in population databases (rs201643709, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with AMT-related conditions. ClinVar contains an entry for this variant (Variation ID: 2126778). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on AMT protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

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