Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

KARS : nonsyndromic genetic deafness

HGNC:6215 | MONDO_0019497
Mode of Inheritance: Autosomal recessive inheritance (HP:0000007)
Expert Panel: Hearing Loss
SOP: Gene Clinical Validity Standard Operating Procedures (SOP), Version 5

Genetic Evidence
Case-Level Data
Evidence Type Case Information Type Guidelines Points PMIDs/Notes
Default Range Max Total Counted
Variant Evidence
Autosomal Dominant or X-linked Disorder Variant is de novo 2 0-3 12
Proband with predicted or proven null variant 1.5 0-2 10
Proband with other variant type with some evidence of gene impact 0.5 0-1.5 7
Autosomal Recessive Disease Two variants in trans and at least one de novo or a predicted/proven null variant 2 0-3 12
1
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5
1
Santos-Cortez RL et al. 2013 Jul 11 (PMID:23768514); Zhou XL et al. 2017 Sep 08. (PMID:28887846);
Segregation Evidence Evidence of segregation in one or more families   Sequencing Method 0-3 3
 
Total LOD Score Canditate Gene Sequencing Exome/Genome or all genes sequenced in linkage region  
2-2.99 0.5 1
3-4.99 1 2
≥5 1.5 3
Case-Control Data
Case-Control Study Type Case-Control Quality Criteria Guidelines Points PMIDs/Notes
Points/Study Max Total Counted
Single Variant Analysis 1. Variant Detection Methodology
2. Power
3. Bias and confounding
4. Statistical Significance
0-6 12
Aggregate Variant Analysis 0-6
Total Genetic Evidence Points (Maximum 12) 1
Experimental Evidence
Evidence Category Evidence Type Guidelines Points PMIDs/Notes
Default Range Max Total Counted
Function Biochemical Function 0.5 0 - 2 2
1
Protein Interaction 0.5 0 - 2 0.5
Lee YN et al. 2004 Feb (PMID:14975237);
Expression 0.5 0 - 2 0.5
Santos-Cortez RL et al. 2013 Jul 11 (PMID:23768514);
Functional Alteration Patient cells 1 0 - 2 2
Non-patient cells 0.5 0 - 1
Models Non-human model organism 2 0 - 4 4
Cell culture model 1 0 - 2
Rescue Rescue in human 2 0 - 4
Rescue in non-human model organism 2 0 - 4
Rescue in cell culture model 1 0 - 2
Rescue in patient cells 1 0 - 2
Total Experimental Evidence Points (Maximum 6) 1

 


 

Assertion criteria Genetic Evidence (0-12 points) Experimental Evidence
(0-6 points)
Total Points
(0-18)
Replication Over Time (Y/N)
Description Case-level, family segregation, or case-control data that support the gene-disease association Gene-level experimental evidence that support the gene-disease association Sum of Genetic & Experimental
Evidence
> 2 pubs w/ convincing evidence over time (>3 yrs)
Assigned Points 1 1 2 NO
CALCULATED CLASSIFICATION LIMITED 1-6
MODERATE 7-11
STRONG 12-18
DEFINITIVE 12-18 AND replication over time
Valid contradictory evidence (Y/N)*
NO
CALCULATED CLASSIFICATION (DATE)
Limited
08/24/2018
EXPERT CURATION (DATE)
Limited
08/24/2018
EVIDENCE SUMMARY
The KARS gene has been associated with autosomal recessive nonsyndromic hearing loss using the ClinGen Clinical Validity Framework as of 10/23/2017. This association was made using case-level data only. At least 4 missense variants have been reported in humans. KARS was first associated with this disease in humans as early as 2013 (Santos-Cortez et al.). Association is seen in at least 4 probands in 2 publications (23768514, 28887846). Variants in this gene segregated with disease in 10 additional family members. This gene-disease association is supported by expression and protein interaction studies. In summary, there is limited evidence to support this gene-disease association. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease association. Variants in KARS have been associated with a wide range of other phenotypes, including peripheral neuropathy, hypertrophic cardiomyopathy, mitochondrial disease, and developmental delays. While linkage analysis provides strong evidence for the DFNB89 locus, there is not strong evidence that KARS is the causative gene in this interval. This classification was approved by the ClinGen Hearing Loss Working Group on 2/27/2018.