Gene Validity Classification Summary

Gene/Disease Pair:

KRAS : Noonan syndrome

HGNC:6407 | MONDO_0018997
Mode of Inheritance: Autosomal dominant inheritance (HP:0000006)
Expert Panel: RASopathy EP
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
20
12
Schubbert S et al. 2006 Mar (PMID:16474405); Carta C et al. 2006 Jul (PMID:16773572); Kratz CP et al. 2009 May (PMID:19396835); Nosan G et al. 2013 Dec (PMID:24382853);
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
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5
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) 12
Experimental Evidence
Evidence Category Evidence Type Guidelines Points PMIDs/Notes
Default Range Max Total Counted
Function Biochemical Function 0.5 0 - 2 2
0.5
Protein Interaction 0.5 0 - 2 0.5
Rauen KA et al. 2013 July 15 (PMID:23875798);
Expression 0.5 0 - 2
Functional Alteration Patient cells 1 0 - 2 2
0
Non-patient cells 0.5 0 - 1 0
Schubbert S et al. 2006 Mar (PMID:16474405); Schubbert S et al. 2007 Nov (PMID:17875937); Razzaque MA et al. 2012 Mar (PMID:22302539); Hernández-Porras I et al. 2014 Nov 18 (PMID:25359213);
Models Non-human model organism 2 0 - 4 4 1 1.5
Razzaque MA et al. 2012 Mar (PMID:22302539); Hernández-Porras I et al. 2014 Nov 18 (PMID:25359213);
Cell culture model 1 0 - 2
Rescue Rescue in human 2 0 - 4
Rescue in non-human model organism 2 0 - 4
0.5
Hernández-Porras I et al. 2014 Nov 18 (PMID:25359213);
Rescue in cell culture model 1 0 - 2
Rescue in patient cells 1 0 - 2
Total Experimental Evidence Points (Maximum 6) 2

 


 

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 12 2 14 YES
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)
Definitive
07/24/2018
EXPERT CURATION (DATE)
Definitive
07/24/2018
EVIDENCE SUMMARY
There is a definitive association between alteration of the KRAS gene and Noonan syndrome (NS) phenotype. The maximum amount of scorable genetic evidence has been published showing de novo as well as non-de novo variants occur in KRAS in patients with NS (Carta et al., 2006; Kratz et al., 2009; Nosan, Bertok, Vesel, Yntema, & Paro-Panjan, 2013; Schubbert et al., 2006). The KRAS gene is also located in the Ras/MAPK pathway which is associated with the Noonan phenotype and variants found in Noonan patients in this gene disrupt the RAS pathway function as demonstrated by both mouse and zebrafish models (Aoki et al., 2016; Hernandez-Porras et al., 2014; Rauen, 2013; Razzaque et al., 2012)