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NM_002109.6(HARS1):c.388G>A (p.Asp130Asn) AND Usher syndrome type 3B

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 17, 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:
RCV002872081.2

Allele description [Variation Report for NM_002109.6(HARS1):c.388G>A (p.Asp130Asn)]

NM_002109.6(HARS1):c.388G>A (p.Asp130Asn)

Gene:
HARS1:histidyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.3
Genomic location:
Preferred name:
NM_002109.6(HARS1):c.388G>A (p.Asp130Asn)
HGVS:
  • NC_000005.10:g.140679796C>T
  • NG_032158.1:g.16591G>A
  • NM_001258040.3:c.268G>A
  • NM_001258041.3:c.388G>A
  • NM_001258042.3:c.268G>A
  • NM_001289092.2:c.301-1781G>A
  • NM_001289093.2:c.181-1781G>A
  • NM_001289094.2:c.301G>A
  • NM_002109.6:c.388G>AMANE SELECT
  • NP_001244969.1:p.Asp90Asn
  • NP_001244970.1:p.Asp130Asn
  • NP_001244971.1:p.Asp90Asn
  • NP_001276023.1:p.Asp101Asn
  • NP_002100.2:p.Asp130Asn
  • LRG_1374t1:c.388G>A
  • LRG_1374:g.16591G>A
  • LRG_1374p1:p.Asp130Asn
  • NC_000005.9:g.140059381C>T
Protein change:
D101N
Molecular consequence:
  • NM_001289092.2:c.301-1781G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001289093.2:c.181-1781G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258040.3:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258041.3:c.388G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258042.3:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289094.2:c.301G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002109.6:c.388G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Usher syndrome type 3B
Synonyms:
USHER SYNDROME, TYPE IIIB
Identifiers:
MONDO: MONDO:0013788; MedGen: C3281066; OMIM: 614504

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003234159Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 17, 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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003234159.2

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 130 of the HARS protein (p.Asp130Asn). 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 expected to disrupt HARS protein function. This variant has not been reported in the literature in individuals affected with HARS-related conditions.

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

Last Updated: Feb 20, 2024