NM_000481.4(AMT):c.159G>A (p.Ala53=) AND Non-ketotic hyperglycinemia

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 29, 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:: RCV001239522.6

Allele description [Variation Report for NM_000481.4(AMT):c.159G>A (p.Ala53=)]

NM_000481.4(AMT):c.159G>A (p.Ala53=)

Gene:

AMT:aminomethyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_000481.4(AMT):c.159G>A (p.Ala53=)

HGVS:

NC_000003.12:g.49422203C>T
NG_015986.1:g.5476G>A
NG_033046.1:g.12122G>A
NM_000481.4:c.159G>AMANE SELECT
NM_001164710.2:c.159G>A
NM_001164711.2:c.90+158G>A
NM_001164712.2:c.159G>A
NP_000472.2:p.Ala53=
NP_001158182.1:p.Ala53=
NP_001158184.1:p.Ala53=
LRG_537t1:c.159G>A
LRG_537:g.5476G>A
NC_000003.11:g.49459636C>T
NC_000003.11:g.49459636C>T
NM_000481.3:c.159G>A
NR_028435.2:n.168G>A

Links:

dbSNP: rs201080782

NCBI 1000 Genomes Browser:

rs201080782

Molecular consequence:

NM_001164711.2:c.90+158G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_028435.2:n.168G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000481.4:c.159G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001164710.2:c.159G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001164712.2:c.159G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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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cytochrome oxidase subunit 1, partial (mitochondrion) [Acromycter perturbator]
cytochrome oxidase subunit 1, partial (mitochondrion) [Acromycter perturbator]
gi|1832106891|gb|QJA14460.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001412398	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002081727	Natera, Inc.	no assertion criteria provided	Uncertain significance (Feb 13, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001412398

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV002081727

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Feb 13, 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, SCV001412398.3

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

#	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., SCV002081727.1

#	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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