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NM_012208.4(HARS2):c.448C>T (p.Arg150Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Oct 27, 2021)
Last evaluated:
Sep 28, 2021
Accession:
VCV000214543.4
Variation ID:
214543
Description:
single nucleotide variant
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NM_012208.4(HARS2):c.448C>T (p.Arg150Cys)

Allele ID
211116
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q31.3
Genomic location
5: 140695556 (GRCh38) GRCh38 UCSC
5: 140075141 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1376:g.9124C>T
LRG_1374:g.831G>A
LRG_1376t1:c.448C>T LRG_1376p1:p.Arg150Cys
... more HGVS
Protein change
R150C, R125C, R80C, R156C
Other names
p.R150C:CGT>TGT
Canonical SPDI
NC_000005.10:140695555:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00005
The Genome Aggregation Database (gnomAD) 0.00009
Trans-Omics for Precision Medicine (TOPMed) 0.00009
Trans-Omics for Precision Medicine (TOPMed) 0.00007
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00006
Links
ClinGen: CA323817
dbSNP: rs140540222
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Sep 28, 2021 RCV000199285.3
Uncertain significance 1 criteria provided, single submitter May 1, 2016 RCV000223531.2
Likely pathogenic 1 no assertion criteria provided May 20, 2019 RCV000782169.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HARS2 - - GRCh38
GRCh37
84 109

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(May 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: not provided
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000271834.2
Submitted: (Mar 21, 2019)
Comment:
Variant classified as Uncertain Significance - Favor Pathogenic. The p.Arg150Cys variant in HARS2 has been reported by our laboratory in one individual with hea ring … (more)
Number of individuals with the variant: 2
Likely pathogenic
(Sep 28, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000251608.11
Submitted: (Oct 27, 2021)
Comment:
Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious … (more)
Likely pathogenic
(May 20, 2019)
no assertion criteria provided
Method: clinical testing
Perrault syndrome 2
Affected status: unknown
Allele origin: paternal, maternal
Molecular Genetics Laboratory,University Hospital Copenhagen
Accession: SCV000920637.1
Submitted: (May 20, 2019)
Comment:
Variants detected in a girl with progressive sensorineural hearing impairment. Signs of premature ovarian failure were uncertain due to her young age.
Comment:
Variant detected as compound heterozygous, together with c.172A>G in three siblings (two girls) with progressive sensorineural hearing impairment. Signs of premature ovarian failure were uncertain … (more)

Observation 1:

Observation 2:

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs140540222...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 08, 2022