Mitochondrial Serine Protease HTRA2 p.G399S in a Female with Di George Syndrome and Parkinson’s Disease
Table 1
List of sequence variants identified.
Locus
Gene
Genotype
HGVSc
HGVSp
SIFT
PolyPhen
Class
Criteria
dbSNP ID
PARK8
LRRK2
hom
NM_198578.3:c.149G>A
NP_940980.3:p.Arg50His
Tolerated (0.61)
Benign (0)
1
BA1
rs2256408
het
NM_198578.3:c.2857T>C
NM_198578.3:c.2857T>C (p.=)
1
BA1
rs7966550
het
NM_198578.3:c.7155A>G
NM_198578.3:c.7155A>G (p.=)
1
BA1
rs33962975
het
NM_198578.3:c.7190T>C
NP_940980.3:p.Met2397Thr
Tolerated (0.71)
Benign (0.001)
1
BA1
rs3761863
PAKK2
PRKN
het
NM_004562.2:c.1138G>C
NP_004553.2:p.Val380Leu
Tolerated (0.83)
Benign (0.001)
1
BA1
rs1801582
PARK17
VPS35
hom
NM_018206.4:c.1938C>T
NM_018206.4:c.1938C>T (p.=)
1
BA1
rs168745
PARK6
PINK1
het
NM_032409.2:c.189C>T
NM_032409.2:c.189C>T (p.=)
1
BA1
rs45530340
hom
NM_032409.2:c.388-7A>G
1
BA1
rs2298298
hom
NM_032409.2:c.960-5G>A
1
BA1
rs3131713
PARK9
ATP13A2
hom
NM_022089.2:c.3516G>A
NM_022089.2:c.3516G>A (p.=)
1
BA1
rs3170740
hom
NM_022089.2:c.3192C>T
NM_022089.2:c.3192C>T (p.=)
1
BA1
rs9435659
hom
NM_022089.2:c.2970G>A
NM_022089.2:c.2970G>A (p.=)
1
BA1
rs761421
hom
NM_022089.2:c.2637C>T
NM_022089.2:c.2637C>T (p.=)
1
BA1
rs9435662
hom
NM_022089.2:c.1815C>T
NM_022089.2:c.1815C>T (p.=)
1
BA1
rs2076603
PARK15
FBXO7
hom
NM_012179.3:c.122+272T>G
1
BA1
rs8137714
hom
NM_012179.3:c.345G>A
NP_036311.3:p.Met115Ile
Tolerated (0.19)
Benign (0)
1
BA1
rs11107
het
NM_012179.3:c.540A>G
NM_012179.3:c.540A>G (p.=)
1
BA1
rs41311141
hom
NM_012179.3:c.949C>T
NM_012179.3:c.949C>T (p.=)
1
BA1
rs9726
SLC52A3
hom
NM_033409.3:c.1233T>C
NM_033409.3:c.1233T>C (p.=)
1
BA1
rs910857
hom
NM_033409.3:c.765C>T
NM_033409.3:c.765C>T (p.=)
1
BA1
rs3746805
het
NM_033409.3:c.321C>T
NM_033409.3:c.321C>T (p.=)
1
BA1
rs3746808
PARK10
ELOVL4
het
NM_022726.3:c.895A>G
NP_073563.1:p.Met299Val
Tolerated (0.92)
Benign (0)
1
BA1
rs3812153
PARK11
GIGYF2
hom
NM_001103147.1:c.3003A>G
NM_001103147.1:c.3003A>G (p.=)
1
BA1
rs3816334
hom
NM_001103147.1:c.3524-9G>A
1
BA1
rs2305137
hom
NM_001103147.1:c.3693_3695delACA
NP_001096617.1:p.Gln1232del
1
BA1
rs10555297
PARK13
HTRA2
het
NM_013247.4:c.1195G>A
NP_037379.1:p.Gly399Ser
Deleterious (0.04)
Probably damaging (0.924)
4
PS3, PP3, PP5
rs72470545
PARK18
EIF4G1
hom
NM_001194947.1:c.502A>G
NP_001181876.1:p.Thr168Ala
Tolerated (0.81)
Benign (0)
1
BA1
rs13319149
hom
NM_001194947.1:c.1315A>G
NP_001181876.1:p.Met439Val
Tolerated (0.36)
Benign (0)
1
BA1
rs2178403
hom
NM_001194947.1:c.3974+9A>C
1
BA1
rs939317
For each variant, the following are reported: locus, gene, genotype detected, HGVS nomenclature (coding and protein, resp., HGVSc and HGVSp), SIFT and PolyPhen prediction (if available), and SNP ID. Furthermore, variants has been classified according to ACMG guidelines in five classes according to Richards et al. [24]. Class and criteria are listed in dedicated columns (BA1: stand-alone evidence of benign impact; PS3: criteria number 3 of strong evidence of pathogenicity; PP3 and PP5: criteria numbers 3 and 5, respectively, of supporting evidence of pathogenicity) [24].
