Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

FANCA : Fanconi anemia complementation group A

HGNC:3582 | MONDO_0009215
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 6
13
12
Fanconi anaemia/Breast cancer consortium et al. 1996 Nov (PMID:8896564); Waisfisz Q et al. 1999 Aug (PMID:10431244); Tipping AJ et al. 2001 May 8 (PMID:11344308);
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5 1
1
Fanconi anaemia/Breast cancer consortium et al. 1996 Nov (PMID:8896564);
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
Nalepa G et al. 2018 Mar (PMID:29376519);
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
Wong JC et al. 2003 Aug 15 (PMID:12913077); Cheng NC et al. 2000 Jul 22 (PMID:10915769);
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
11/09/2018
EXPERT CURATION (DATE)
Definitive
12/21/2018
EVIDENCE SUMMARY
There is abundant evidence published associating the FANCA gene with Fanconi anemia complementation group A, since the gene-disease relationship was first proposed by Fanconi Anaemia/Breast Cancer Consortium (1996). Multiple case level studies have been performed with FA patients that have variants in the FANCA gene. Eight of the FA proteins (FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, and FANCM) are part of a nuclear multiprotein core complex which triggers activating monoubiquitination of the FANCD2 in the FA/BRCA DNA repair pathway. Multiple Fanca deficient mouse models have been established to show consistent phenotypes with FA patients including growth retardation, microphthalmia, craniofacial malformations, and hypogonadism. All of these types of evidence are consistent with a definitive relationship between the FANCA gene and Fanconi anemia complementation group A.