Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

HOMER2 : nonsyndromic genetic deafness

HGNC:17513 | MONDO_0019497
Mode of Inheritance: Autosomal dominant inheritance (HP:0000006)
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 1 1 1
Lu X et al. 2018 Jul 26. (PMID:30047143);
Proband with other variant type with some evidence of gene impact 0.5 0-1.5 7 1
1
1
Azaiez H et al. 2015 Mar (PMID:25816005);
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   Summed LOD Family Count 3 3  
Candidate gene sequencing
Exome/genome or all genes sequenced in linkage region 5.11 2
Azaiez H et al. 2015 Mar (PMID:25816005); Lu X et al. 2018 Jul 26. (PMID:30047143);
Total Summed LOD Score 5.11    
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
Protein Interaction 0.5 0 - 2 1 0.5
Lu X et al. 2018 Jul 26. (PMID:30047143);
Expression 0.5 0 - 2 1 0.5
Azaiez H et al. 2015 Mar (PMID:25816005);
Functional Alteration Patient cells 1 0 - 2 2
0.5
Non-patient cells 0.5 0 - 1 1 0.5
Lu X et al. 2018 Jul 26. (PMID:30047143);
Models Non-human model organism 2 0 - 4 4 2 3 3
Azaiez H et al. 2015 Mar (PMID:25816005);
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) 4.5

 


 

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 4.5 9.5 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
10/16/2018
EXPERT CURATION (DATE)
Moderate
10/16/2018
EVIDENCE SUMMARY
The HOMER2 gene has been associated with autosomal dominant nonsyndromic hearing loss using the ClinGen Clinical Validity Framework as of 9/20/18. This association was made using case-level data only. At least 1 missense variant and 1 frameshift variant have been reported in humans. HOMER2 was first associated with this disease in humans as early as 2015 (Azaiez et al.). Association is seen in two probands in 2 publication (25816005, 30047143). Variants in this gene segregated with disease in 17 additional family members. This gene-disease association is supported by a knock-out mouse model with profound deafness and a zebrafish injected with synthetic mRNA encoding the human missense variant, which suggest a dominant-negative effect (25816005). Additionally, a protein interaction study demonstrates the frameshift variant's affect on the protein's ability to multimerize (30047143). 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 10/16/18.