|
|
Evidence Type |
Case Information Type |
Guidelines |
Scores |
PMIDs/Notes |
| Default |
Range |
Max |
Points |
Tally |
|
Autosomal Dominant or X-linked Disorder |
Variant is de novo |
2 |
0-3 |
12 |
0.0
|
0 |
|
| Proband with predicted or proven null variant |
1.5 |
0-2 |
10 |
0.0 |
0 |
|
| Proband with other variant type with some evidence of gene impact |
0.5 |
0-1.5 |
7 |
2.0 |
2
|
Wang L et al. 2010 Nov 12 (PMID:21055718); Ziganshin BA et al. 2015 Nov (PMID:26188975); Proost D et al. 2015 Aug (PMID:25907466); (PMID 21055718: Panel sequencing of a few candidate genes in 94 probands from families with thoracic aortic aneurysm and aortic dissection (TAAD). 1 variant in MYLK absent in ethnically matched controls (+ 4 others) p.S1759P. Also identified a p.R1480X in an unrelated proband. Additional 3 variants in 3 other probands: p.A1754T, p.V1213M p.E1399K not present in ethnically-matched controls but no family data . Points =1 due to lack of gene impact evidence (ignored the latter three missense variants).
PMID 26188975: Found a mutation (p.P1759S) reported earlier in 1 proband; segregated with disease in her family. Points= 0.5
PMID 25907466: Identified one proband with p.R1487* . Points=0.5
)
|
| Autosomal Recessive Disease |
Two variants in trans and at least one de novo or a predicted/proven null variant |
2 |
0-3 |
12 |
0.0 |
0 |
|
| Two variants (not predicted/proven null) with some evidence of gene impact in trans |
1 |
0-1.5 |
0.0 |
| Segregation Evidence |
Evidence of segregation in one or more families |
LOD Score Examples |
3 |
5 |
0-7 |
7 |
4.0 |
4 |
Wang L et al. 2010 Nov 12 (PMID:21055718); Ziganshin BA et al. 2015 Nov (PMID:26188975); (PMID 21055718: Panel sequencing of a few candidate genes in 94 probands from families with TAAD
1 variant in MYLK absent in ethnically matched controls (+ 4 others) p.S1759P segregated with disease in family (3 probands).
Further sequencing of MYLK in 99 probands with additional TAAD – found another variant
(p.R1480X) that segregated with disease in family LOD score 1.2 (increased to 1.8 with addition of family members who had sudden death) Points 3
PMID 26188975: weak segregation data. Less than 4 convincing segregations. 1 point.)
|
| 2 |
4 |
| 1.5 |
3 |
| 1 |
1.5 |
| |
|
|
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 |
0.0 |
|
|
| Aggregate Variant Analysis |
0-6 |
12 |
0.0 |
|
|
| Total Genetic Evidence Points (Maximum 12) |
6 |
|
|
Evidence Category |
Evidence Type |
Guidelines |
Scores |
PMIDs/Notes |
| Default |
Range |
Max |
Points |
Tally |
| Function |
Biochemical Function |
0.5 |
0 - 2 |
2 |
2.0 |
2 |
Gao N et al. 2013 Mar 15 (PMID:23362260); Basu S et al. 2013 Apr 19 (PMID:23482558); Basu S et al. 2016 Feb 5 (PMID:26703474); (PMID 23362260: A 50% decrease in MLCK (=MYLK) in aortic smooth muscle resulted in 40% inhibition of myosin regulatory light chain phosphorylation and aorta contractile responses, whereas a 90% decrease profoundly inhibited both responses.
PMID 23482558: Demonstrated that NOTCH1 induced MYLK expression. Knocked out NOTCH1 signaling in vascular smooth muscle cells (vSMC) in mice. This reduced MYLK expression and activity. Supported by report of NOTCH1-responsive element in MYLK promoter
PMID 26703474 showed co-immunoprecipitation of MYLK promoter and JAGGED1 ligand & also MYLK promoter with NOTCH1-enhanced myocardin/SRF complex, & demonstrated each of these enhanced MYLK expression.) |
| Protein Interaction |
0.5 |
0 - 2 |
| Expression |
0.5 |
0 - 2 |
| Functional Alteration |
Patient cells |
1 |
0 - 2 |
2 |
1.0 |
1 |
Wang L et al. 2010 Nov 12 (PMID:21055718); (Patient cells:
Authors transfected COS7 cells with mutations p.S1759P and p.A1754T. Demonstrated significantly reduced (p.1754T) ) or abolished (p.S1759P) calmodulin binding in transfected cells & reduced kinase activity.
)
|
| Non-patient cells |
0.5 |
0 - 1 |
| Models & Rescue |
Animal model |
2 |
0 - 4 |
4 |
2.0 |
2 |
Wang L et al. 2010 Nov 12 (PMID:21055718); (Authors generated a tamoxifen-induced, SMC specific knockout of MYLK & examined aortas after 13 days.
Increased proteoglycan deposition in aortic media
Increased collagen deposition in adventitia
Increased expression of MMP2
No aortic phenotype (mice with SMC – specific k/o usually die due to low BP, reduced gut mobility, airway constriction and urinary dysfunction) - note low BP similar to ACTA2 k/o effects
) |
| 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) |
5 |
|