Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

DDB2 : xeroderma pigmentosum group E

HGNC:2718 | MONDO_0010213
Mode of Inheritance: Autosomal recessive inheritance (HP:0000007)
Expert Panel: Hereditary Cancer
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 3
6
12
Itoh T et al. 1999 Aug (PMID:10469312); Rapić-Otrin V et al. 2003 Jul 1 (PMID:12812979);
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5 6
6
Nichols AF et al. 1996 Oct 4 (PMID:8798680); Rapić-Otrin V et al. 2003 Jul 1 (PMID:12812979); Oh KS et al. 2011 Mar (PMID:21107348);
Segregation Evidence   Summed LOD Family Count  
Candidate gene sequencing
Exome/genome or all genes sequenced in linkage region
Total Summed LOD Score    
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) 12
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
2
2
Schubert S et al. 2014 Jul (PMID:24105368);
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 Non-human model organism 2 0 - 4 4 2 4 4
Itoh T et al. 2004 Feb 17 (PMID:14769931); Yoon T et al. 2005 Jan 13 (PMID:15558025);
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) 6

 


 

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 6 18 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
11/02/2018
EXPERT CURATION (DATE)
Definitive
11/02/2018
EVIDENCE SUMMARY
There is abundant evidence published associating the DDB2 gene with xeroderma pigmentosum group E since the gene-disease relationship was first proposed by Nichols et al. (1996). Multiple case level studies have been performed with XPE patients that have variants in the DDB2 gene. 8 complementation groups genes (XPA, XPB, XPC, XPD, XPE, XPF, XPG, and XP variant (XPV)) in Nucleotide excision repair (NER) pathway were reported to cause Xeroderma Pigmentosum. Multiple DDB2 deficient mouse models have been established to show consistent phenotypes with XPG patients, including significantly enhanced skin carcinogenesis in response to UV-irradiation, reduced life span and the development of spontaneous malignant tumors. All of these types of evidence are consistent with a definitive relationship between the DDB2 gene and xeroderma pigmentosum group E.