NM_000481.4(AMT):c.148G>C (p.Val50Leu) AND Non-ketotic hyperglycinemia

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 14, 2022
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:: RCV001247646.5

Allele description [Variation Report for NM_000481.4(AMT):c.148G>C (p.Val50Leu)]

NM_000481.4(AMT):c.148G>C (p.Val50Leu)

Gene:

AMT:aminomethyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_000481.4(AMT):c.148G>C (p.Val50Leu)

HGVS:

NC_000003.12:g.49422214C>G
NG_015986.1:g.5465G>C
NG_033046.1:g.12111G>C
NM_000481.4:c.148G>CMANE SELECT
NM_001164710.2:c.148G>C
NM_001164711.2:c.90+147G>C
NM_001164712.2:c.148G>C
NP_000472.2:p.Val50Leu
NP_001158182.1:p.Val50Leu
NP_001158184.1:p.Val50Leu
LRG_537t1:c.148G>C
LRG_537:g.5465G>C
NC_000003.11:g.49459647C>G
NC_000003.11:g.49459647C>G
NM_000481.3:c.148G>C
NR_028435.2:n.157G>C

Protein change:

V50L

Links:

dbSNP: rs148917929

NCBI 1000 Genomes Browser:

rs148917929

Molecular consequence:

NM_001164711.2:c.90+147G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000481.4:c.148G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001164710.2:c.148G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001164712.2:c.148G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_028435.2:n.157G>C - 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
SCV001421081	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 14, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002081729	Natera, Inc.	no assertion criteria provided	Uncertain significance (Oct 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001421081

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 14, 2022)

germline

clinical testing

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

SCV002081729

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Oct 16, 2020)

germline

clinical testing

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, SCV001421081.2

#	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 leucine, which is neutral and non-polar, at codon 50 of the AMT protein (p.Val50Leu). This variant is present in population databases (rs148917929, gnomAD 0.02%). 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: 971783). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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

From Natera, Inc., SCV002081729.1

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

#	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

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