NM_005548.3(KARS1):c.433T>C (p.Tyr145His) AND Leukoencephalopathy, progressive, infantile-onset, with or without deafness

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 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:: RCV001807772.1

Allele description [Variation Report for NM_005548.3(KARS1):c.433T>C (p.Tyr145His)]

NM_005548.3(KARS1):c.433T>C (p.Tyr145His)

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.433T>C (p.Tyr145His)

HGVS:

NC_000016.10:g.75636503A>G
NG_028025.1:g.16185T>C
NM_001130089.2:c.517T>C
NM_001378148.1:c.-36T>C
NM_005548.3:c.433T>CMANE SELECT
NP_001123561.1:p.Tyr173His
NP_001123561.1:p.Tyr173His
NP_005539.1:p.Tyr145His
LRG_366t1:c.517T>C
LRG_366:g.16185T>C
LRG_366p1:p.Tyr173His
NC_000016.9:g.75670401A>G
NM_001130089.1:c.517T>C
p.(Tyr173His)

Protein change:

Y145H; TYR173HIS

Links:

OMIM: 601421.0003; dbSNP: rs397514745

NCBI 1000 Genomes Browser:

rs397514745

Molecular consequence:

NM_001378148.1:c.-36T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001130089.2:c.517T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005548.3:c.433T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Leukoencephalopathy, progressive, infantile-onset, with or without deafness
Identifiers:: MONDO: MONDO:0030893; MedGen: C5542996; OMIM: 619147

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002058683	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002058683

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 3, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical 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 3billion, SCV002058683.1

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

Description

Same nucleotide change resulting in same amino acid change has been previously reported to be associated with KARS1 related disorder (ClinVar ID: VCV000060752, PS1_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000028, PM2_M). A missense variant is a common mechanism associated with Leukoencephalopathy (PP2_P).Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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