Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

PTPRQ : Sensorineural hearing loss

HGNC:9679 | OrphaNet: ORPHA90636 | OMIM:603317
Mode of Inheritance: Autosomal recessive inheritance (HP:0000007)

Genetic Evidence
Case-Level Data
Evidence Type Case Information Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
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 4.0 5.5
Schraders M et al. 2010 Apr 9 (PMID:20346435); Shahin H et al. 2010 Sep (PMID:20472657); Gao X et al. 2015 (PMID:25919374);
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5 1.5
Segregation Evidence Evidence of segregation in one or more families LOD Score Examples 3 5 0-7 7 8.0 7
Schraders M et al. 2010 Apr 9 (PMID:20346435); Shahin H et al. 2010 Sep (PMID:20472657); Gao X et al. 2015 (PMID:25919374);
2 4
1.5 3
1 1.5
   
Case-Control Data
Case-Control Study Type Case-Control Quality Criteria Guidelines Scores PMIDs/Notes
Points/Study Max Points Tally
Single Variant Analysis 1. Variant Detection Methodology
2. Power
3. Bias and confounding
4. Statistical Significance
0-6 12
Aggregate Variant Analysis 0-6 12
Total Genetic Evidence Points (Maximum 12) 12
Experimental Evidence
Evidence Category Evidence Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
Function Biochemical Function 0.5 0 - 2 2 2.0 2
Goodyear RJ et al. 2003 Oct 8 (PMID:14534255); Sakaguchi H et al. 2008 Jul (PMID:18412156); Salles FT et al. 2014 Jan (PMID:24285636); Chen J et al. 2014 Mar (PMID:24446963);
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2
Functional Alteration Patient cells 1 0 - 2 2
Non-patient cells 0.5 0 - 1
Models & Rescue Animal model 2 0 - 4 4 2.0 2
Goodyear RJ et al. 2003 Oct 8 (PMID:14534255); Goodyear RJ et al. 2012 Feb 22 (PMID:22357859);
Cell culture model system 1 0 - 2
Rescue in animal model 2 0 - 4
Rescue in engineered equivalent 1 0 - 2
Total Experimental Evidence Points (Maximum 6) 4

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 4 16 YES
CALCULATED CLASSIFICATION LIMITED 1-6
MODERATE 7-11
STRONG 12-18
DEFINITIVE 12-18 AND replication over time
Valid contradictory evidence (Y/N)*
CALCULATED CLASSIFICATION (DATE)
DEFINITIVE
10/25/2016
EXPERT CURATION (DATE)
DEFINITIVE
02/23/2017