Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome
Table 2
Identified SNVs and their predictions in the present sample (n = 60).
Variant Nomeclature
NG_023054.2: g.109490C > T
NM_002745.5: c.1037
NM_002745.5: c.310
NC_000011.10: 134150005: T: C
Gene
MAPK1
MAPK1
MAPK1
JAM3
Position (hg19)
22: 22117480
22: 22117502
22: 22118229
11: 134019901
dbSNP (b151)
rs897688340
rs13058
rs41282607
rs7936421
MAF (AbraOM)
Not identified in Brazillian population
0.050296
Not identified in Brazillian population
0.153285
MAF (gnoMAD)
0.00000
0.050024
0.021495
0.162251
Location
UTR3
UTR3
UTR3
UTR3
CADD
32
31
24.3
17.07
FATHMM-XL
0.888171
0.887487
0.779486
0.803652
RegulomeDB
Likely to affect binding
Likely to affect binding
Less likely to affect binding
Likely to affect binding
SIFT
NA
NA
NA
NA
eQTLS e GTEX
NA
Artery tibial
Stomach/thyroid
Artery aorta/muscle skeletal
GRASP/trait
NA
Yes/microalbuminuria
NA
Yes/aortic valve
ORegAnno
NA
Transcription factor binding site
Transcription factor binding site
NA
miRNA-target
NA
NA
MAPK1: miR-217
NA
Patients
1 with cardiac malformation
1 with immuno/psychiatric alteration
1 with cardiac malformation
16 with variable phenotype
According to the Human Genome Variation Society; Variant ID from dbSNP (b151); MAF: minor allele frequency, SIFT score: a score <0.5 is considered deleterious; Combined Annotation Dependent Depletion (CADD): a score of 20 means that a variant is amongst the top 1% of deleterious variant; FATHMM-XL: 0 to 1. Scores nearer 1 are more likely to be deleterious.
