NM_020745.4(AARS2):c.2702G>A (p.Arg901Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 29, 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:: RCV002041361.14

Allele description [Variation Report for NM_020745.4(AARS2):c.2702G>A (p.Arg901Gln)]

NM_020745.4(AARS2):c.2702G>A (p.Arg901Gln)

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.2702G>A (p.Arg901Gln)

HGVS:

NC_000006.12:g.44301247C>T
NG_028283.4:g.789160C>T
NG_031952.2:g.17100G>A
NM_020745.4:c.2702G>AMANE SELECT
NP_065796.2:p.Arg901Gln
NC_000006.11:g.44268984C>T
NG_031952.1:g.17080G>A
NM_020745.2:c.2702G>A

Protein change:

R901Q

Links:

dbSNP: rs768583871

NCBI 1000 Genomes Browser:

rs768583871

Molecular consequence:

NM_020745.4:c.2702G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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5-hydroxytryptamine receptor 3D isoform 3 precursor [Homo sapiens]
5-hydroxytryptamine receptor 3D isoform 3 precursor [Homo sapiens]
gi|254692968|ref|NP_001157118.1|

Protein
5-HT3c1 serotonin receptor-like protein [Homo sapiens]
5-HT3c1 serotonin receptor-like protein [Homo sapiens]
gi|37574912|gb|AAQ93476.1|

Protein
5-hydroxytryptamine serotonin receptor 3D [Homo sapiens]
5-hydroxytryptamine serotonin receptor 3D [Homo sapiens]
gi|110431740|gb|AAO38166.2|

Protein
Mycobacterium tuberculosis 2094HD, whole genome shotgun sequencing project
Mycobacterium tuberculosis 2094HD, whole genome shotgun sequencing project
gi|621127257|gb|JKBD00000000.1|JKBD 000

Nucleotide
RecName: Full=5-hydroxytryptamine receptor 3C; Short=5-HT3-C; Short=5-HT3C; AltN...
RecName: Full=5-hydroxytryptamine receptor 3C; Short=5-HT3-C; Short=5-HT3C; AltName: Full=Serotonin receptor 3C; Flags: Precursor
gi|166198366|sp|Q8WXA8.2|5HT3C_HUMA

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002114193	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 29, 2022)	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

SCV002114193

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 29, 2022)

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, SCV002114193.3

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

Description

This variant has not been reported in the literature in individuals affected with AARS2-related conditions. 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. 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) performed at Invitae indicates that this missense variant is not expected to disrupt AARS2 protein function. This variant is present in population databases (rs768583871, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 901 of the AARS2 protein (p.Arg901Gln).

#	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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