NM_020320.5(RARS2):c.1390C>T (p.Gln464Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 22, 2023
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:: RCV003094037.3

Allele description [Variation Report for NM_020320.5(RARS2):c.1390C>T (p.Gln464Ter)]

NM_020320.5(RARS2):c.1390C>T (p.Gln464Ter)

Gene:

RARS2:arginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q15

Genomic location:

Preferred name:

NM_020320.5(RARS2):c.1390C>T (p.Gln464Ter)

HGVS:

NC_000006.12:g.87518655G>A
NG_008601.1:g.76363C>T
NM_001318785.2:c.865C>T
NM_001350505.2:c.1390C>T
NM_001350506.2:c.865C>T
NM_001350507.2:c.865C>T
NM_001350508.2:c.865C>T
NM_001350509.2:c.865C>T
NM_001350510.2:c.865C>T
NM_001350511.2:c.865C>T
NM_020320.5:c.1390C>TMANE SELECT
NP_001305714.1:p.Gln289Ter
NP_001337434.1:p.Gln464Ter
NP_001337435.1:p.Gln289Ter
NP_001337436.1:p.Gln289Ter
NP_001337437.1:p.Gln289Ter
NP_001337438.1:p.Gln289Ter
NP_001337439.1:p.Gln289Ter
NP_001337440.1:p.Gln289Ter
NP_064716.2:p.Gln464Ter
NC_000006.11:g.88228373G>A
NC_000006.11:g.88228373G>A
NR_134857.2:n.1416C>T
NR_146738.2:n.1688C>T
NR_146739.2:n.1497C>T
NR_146740.2:n.1765C>T
NR_146741.2:n.1427C>T
NR_146742.2:n.1799C>T
NR_146743.2:n.1637C>T
NR_146744.2:n.1765C>T
NR_146745.2:n.1424C>T
NR_146746.2:n.1859C>T
NR_146747.2:n.1203C>T
NR_146748.2:n.1663C>T
NR_146749.2:n.1637C>T
NR_146750.2:n.1761C>T
NR_146751.2:n.1641C>T
NR_146752.2:n.1705C>T
NR_146753.2:n.1557C>T
NR_146754.2:n.1501C>T
NR_146755.2:n.1765C>T
NR_146756.2:n.1420C>T
NR_146757.2:n.1691C>T
NR_146758.2:n.1420C>T
NR_146759.2:n.1420C>T

Protein change:

Q289*

Links:

dbSNP: rs753312969

NCBI 1000 Genomes Browser:

rs753312969

Molecular consequence:

NR_134857.2:n.1416C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146738.2:n.1688C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146739.2:n.1497C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146740.2:n.1765C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146741.2:n.1427C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146742.2:n.1799C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146743.2:n.1637C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146744.2:n.1765C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146745.2:n.1424C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146746.2:n.1859C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146747.2:n.1203C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146748.2:n.1663C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146749.2:n.1637C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146750.2:n.1761C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146751.2:n.1641C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146752.2:n.1705C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146753.2:n.1557C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146754.2:n.1501C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146755.2:n.1765C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146756.2:n.1420C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146757.2:n.1691C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146758.2:n.1420C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146759.2:n.1420C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001318785.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350505.2:c.1390C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350506.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350507.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350508.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350509.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350510.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350511.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_020320.5:c.1390C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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100360302[uid] AND (alive[prop]) (1)
Gene
Sec16a SEC16 homolog A, endoplasmic reticulum export factor [Rattus norvegicus]
Sec16a SEC16 homolog A, endoplasmic reticulum export factor [Rattus norvegicus]
Gene ID:100360302

Gene
Dyssomnias
Dyssomnias
A broad category of sleep disorders characterized by either hypersomnolence or insomnia. The three major subcategories include intrinsic (i.e., arising from within the body) (...<br/>Year introduced: 2000

MeSH
D020920 (1)
MeSH
RecName: Full=Cell division cycle 7-related protein kinase; Short=CDC7-related k...
RecName: Full=Cell division cycle 7-related protein kinase; Short=CDC7-related kinase; Short=muCdc7
gi|341940339|sp|Q9Z0H0.2|CDC7_MOUSE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003441225	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 22, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 17847012, 22569581, 26083569, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003441225

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 22, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Deleterious mutation in the mitochondrial arginyl-transfer RNA synthetase gene is associated with pontocerebellar hypoplasia.

Edvardson S, Shaag A, Kolesnikova O, Gomori JM, Tarassov I, Einbinder T, Saada A, Elpeleg O.

Am J Hum Genet. 2007 Oct;81(4):857-62. Epub 2007 Aug 24.

PubMed [citation]

PMID:: 17847012
PMCID:: PMC2227936

Pontocerebellar hypoplasia type 6 caused by mutations in RARS2: definition of the clinical spectrum and molecular findings in five patients.

Cassandrini D, Cilio MR, Bianchi M, Doimo M, Balestri M, Tessa A, Rizza T, Sartori G, Meschini MC, Nesti C, Tozzi G, Petruzzella V, Piemonte F, Bisceglia L, Bruno C, Dionisi-Vici C, D'Amico A, Fattori F, Carrozzo R, Salviati L, Santorelli FM, Bertini E.

J Inherit Metab Dis. 2013 Jan;36(1):43-53. doi: 10.1007/s10545-012-9487-9. Epub 2012 May 8.

PubMed [citation]

PMID:: 22569581

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003441225.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is present in population databases (rs753312969, gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RARS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1686119). For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Gln464*) in the RARS2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RARS2 are known to be pathogenic (PMID: 17847012, 22569581, 26083569).

#	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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