Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

HGF : nonsyndromic genetic deafness

HGNC:4893 | MONDO_0019497
Mode of Inheritance: Autosomal recessive inheritance (HP:0000007)
Expert Panel: Hearing Loss
SOP: Gene Clinical Validity Standard Operating Procedures (SOP), Version 6

Genetic Evidence
Case-Level Data
Evidence Type Case Information Type Guidelines Points PMIDs/Notes
Default Range Max Count 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
2
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5 3
2
Schultz JM et al. 2009 Jul (PMID:19576567);
Segregation Evidence   Summed LOD Family Count 3 3  
Candidate gene sequencing
Exome/genome or all genes sequenced in linkage region 5 1
Schultz JM et al. 2009 Jul (PMID:19576567);
Total Summed LOD Score 5    
Case-Control Data
Case-Control Study Type Case-Control Quality Criteria Guidelines Points PMIDs/Notes
Points/Study Max Count Points 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) 5
Experimental Evidence
Evidence Category Evidence Type Guidelines Points PMIDs/Notes
Default Range Max Count Total Counted
Function Biochemical Function 0.5 0 - 2 2 1
0.5
1
Shibata S et al. 2016 Aug 3 (PMID:27488639);
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2 1 0.5
Shibata S et al. 2016 Aug 3 (PMID:27488639);
Functional Alteration Patient cells 1 0 - 2 2
Non-patient cells 0.5 0 - 1
Models Non-human model organism 2 0 - 4 4 3 5 4
Schultz JM et al. 2009 Jul (PMID:19576567); Shibata S et al. 2016 Aug 3 (PMID:27488639);
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) 5

 


 

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 5 5 10 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)
Moderate
10/04/2018
EXPERT CURATION (DATE)
Moderate
01/16/2018
EVIDENCE SUMMARY
The HGF gene has been associated with autosomal recessive nonsyndromic hearing loss using the ClinGen Clinical Validity Framework as of 10/20/2017. This association was made using case-level data only. At least 3 variants have been reported in humans. HGF was first associated with this disease in humans as early as 2009 (Schultz et al.). Association is seen in 39 families in 1 publication, however detailed information is not provided in terms of segregation (Schultz et al. 2009). This gene-disease association is supported by multiple mouse models (Schultz et al. 2009, Shibata et al. 2016). In summary, there is moderate evidence to support this gene-disease association. While more evidence is needed to establish this association definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Hearing Loss Working Group on 1/16/2018.