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NM_005548.3(KARS1):c.421A>C (p.Lys141Gln) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 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:
RCV003318463.1

Allele description [Variation Report for NM_005548.3(KARS1):c.421A>C (p.Lys141Gln)]

NM_005548.3(KARS1):c.421A>C (p.Lys141Gln)

Gene:
KARS1:lysyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q23.1
Genomic location:
Preferred name:
NM_005548.3(KARS1):c.421A>C (p.Lys141Gln)
HGVS:
  • NC_000016.10:g.75636515T>G
  • NG_028025.1:g.16173A>C
  • NM_001130089.2:c.505A>C
  • NM_001378148.1:c.-48A>C
  • NM_005548.3:c.421A>CMANE SELECT
  • NP_001123561.1:p.Lys169Gln
  • NP_001123561.1:p.Lys169Gln
  • NP_005539.1:p.Lys141Gln
  • LRG_366t1:c.505A>C
  • LRG_366:g.16173A>C
  • LRG_366p1:p.Lys169Gln
  • NC_000016.9:g.75670413T>G
  • NM_001130089.1:c.505A>C
Protein change:
K141Q
Links:
dbSNP: rs761347066
NCBI 1000 Genomes Browser:
rs761347066
Molecular consequence:
  • NM_001378148.1:c.-48A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001130089.2:c.505A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005548.3:c.421A>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 89
Synonyms:
Deafness, autosomal recessive 89
Identifiers:
MONDO: MONDO:0013489; MedGen: C3151351; Orphanet: 90636; OMIM: 613916
Name:
Leukoencephalopathy, progressive, infantile-onset, with or without deafness
Identifiers:
MONDO: MONDO:0030893; MedGen: C5542996; OMIM: 619147

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004021284Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 2, 2022) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownno1not 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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV004021284.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The c.505A>C variant is not present in publicly available population databases like, 1000 Genomes, EVS and Indian Exome Database. The heterozygous state of the variant is present in ExAC and gnomAD, at a low frequency. The variant is not present in our in-house exome database. The variant was not previously reported to Clinvar, HGMD and/or OMIM database, in any affected individuals. In-silico pathogenicity prediction programs like SIFT, PolyPhen-2, MutationTaster2, CADD etc. predicted this variant to be likely disease causing, however these predictions were not confirmed by any published functional studies. This variant has been identified in an individual as a part of carrier screening in view of early deaths of two previous offspring with noted abnormalities.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnonot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023