NM_020745.4(AARS2):c.2T>C (p.Met1Thr) AND Inborn genetic diseases

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 9, 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:: RCV002897416.8

Allele description [Variation Report for NM_020745.4(AARS2):c.2T>C (p.Met1Thr)]

NM_020745.4(AARS2):c.2T>C (p.Met1Thr)

Gene:

AARS2:alanyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_020745.4(AARS2):c.2T>C (p.Met1Thr)

HGVS:

NC_000006.12:g.44313322A>G
NG_028283.4:g.801235A>G
NG_031952.2:g.5025T>C
NG_108354.1:g.331A>G
NM_020745.4:c.2T>CMANE SELECT
NP_065796.2:p.Met1Thr
NC_000006.11:g.44281059A>G
NG_031952.1:g.5005T>C
NM_020745.2:c.2T>C

Protein change:

M1T

Molecular consequence:

NM_020745.4:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_020745.4:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003651455	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Nov 9, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003651455

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Nov 9, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV003651455.3

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

Description

The c.2T>C (p.M1?) alteration is located in coding exon 1 of the AARS2 gene and results from a T to C substitution at nucleotide position 1. This alters the methionine residue at the initiation codon (ATG). Sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame._x000D_ _x000D_ Based on the available evidence, the AARS2 c.2T>C (p.M1?) alteration is classified as likely pathogenic for autosomal recessive mitochondrial alanyl-tRNA synthetase deficiency; however, its clinical significance for autosomal recessive AARS2-related combined oxidative phosphorylation deficiency is unclear. Based on the available evidence, this alteration is classified as likely pathogenic.

#	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 1, 2024

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