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NM_012208.4(HARS2):c.1450_1451delinsC (p.Ser484fs) AND Perrault syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 2, 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:
RCV002471585.2

Allele description [Variation Report for NM_012208.4(HARS2):c.1450_1451delinsC (p.Ser484fs)]

NM_012208.4(HARS2):c.1450_1451delinsC (p.Ser484fs)

Gene:
HARS2:histidyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
5q31.3
Genomic location:
Preferred name:
NM_012208.4(HARS2):c.1450_1451delinsC (p.Ser484fs)
HGVS:
  • NC_000005.10:g.140698067_140698068delinsC
  • NG_021415.1:g.11635_11636delinsC
  • NM_001278731.2:c.1375_1376delinsC
  • NM_001278732.2:c.1018_1019delinsC
  • NM_001363535.2:c.1468_1469delinsC
  • NM_001363536.2:c.1240_1241delinsC
  • NM_012208.4:c.1450_1451delinsCMANE SELECT
  • NP_001265660.1:p.Ser459fs
  • NP_001265661.1:p.Ser340fs
  • NP_001350464.1:p.Ser490fs
  • NP_001350465.1:p.Ser414fs
  • NP_036340.1:p.Ser484fs
  • LRG_1376t1:c.1450_1451delinsC
  • LRG_1376:g.11635_11636delinsC
  • LRG_1376p1:p.Ser484fs
  • NC_000005.9:g.140077652_140077653delinsC
  • NM_012208.3:c.1450_1451delAGinsC
Protein change:
S340fs
Molecular consequence:
  • NM_001278731.2:c.1375_1376delinsC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001278732.2:c.1018_1019delinsC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001363535.2:c.1468_1469delinsC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001363536.2:c.1240_1241delinsC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012208.4:c.1450_1451delinsC - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Perrault syndrome 2 (PRLTS2)
Identifiers:
MONDO: MONDO:0013972; MedGen: C3554105; Orphanet: 2855; OMIM: 614926

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002768963Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Feb 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768963.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A heterozygous deletion variant was identified, NM_012208.3(HARS2):c.1450_1451delinsC in exon 12 of 13 of the HARS2 gene. This deletion is predicted to cause a frameshift from amino acid position 484 introducing a stop codon 35 residues downstream, NP_036340.1(HARS2):p.(Ser484Profs*35), resulting in an extension of the reading frame. The variant is present in the gnomAD population database at a frequency of 0.0025% (7 heterozygotes, 0 homozygotes). It has not been previously observed in clinical cases. No other variants predicted to cause an extension of the reading frame have been reported in a clinical testing setting. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024