Table 2 Genetic variants that might be responsible for the observed phenotype in the studied family
Gene name/chromosome | SNP Reference number | Frequency of change* MAF/minor Allele count | Change of nucleotide/amino acid residue HGVS names | Inheritance patients/asymptomatic family members (WES) | Clinical significance ClinVar NCBI | |||
|---|---|---|---|---|---|---|---|---|
RK | MK | EK | AK | |||||
NT5C3A chr7 | rs1227859962 | delACA = 0.000014 (2/140214, GnomAD) delACA = 0.00007 (1/15150, ALFA) delACA = 0.0002 (1/4480, Estonian) | NM_001002010.2:c.597_599delGTT NP_001361265.1:p.Phe149del | het | het | abs | abs | Not reported |
TYMP chr22 and SCO2 chr22 | rs11479 | A = 0.087629 (12223/139486, ALFA) A = 0.1428 (715/5008, 1000G) A = 0.1105 (495/4480, Estonian) | TYMP NM_001113755.2:c.1412C > T NP_001107227.1:p.Ser471Leu SCO2 (nearGene-5) NM_005138.2:c.-349C > T | het | het | het | abs | Benign (10 July 2021) |
rs112723255 | T = 0.045881 (10439/227524, GnomAD_exome) T = 0.04446 (2148/48310, ALFA) T = 0.0569 (255/4480, Estonian) | TYMP NM_001113755.2:c.1393G > A NP_001107227.1:p.Ala465Thr SCO2 (nearGene-5) NM_005138.2:c.-368G > A | het | het | abs | het | Benign/ Likely benign (31 July 2021) | |
PUDP chrX | rs187333600 | A = 0.014659 (3880/264690, TOPMED) A = 0.018758 (1934/103104, GnomAD) A = 0.02251 (615/27324, ALFA) | UTR-5 NM_001135565.1:c.-14C > T | hom | hom | het | abs | Not reported |
HCFC1 chrX | rs1557112939 | None | NM_005334.2:c.4759T > C NP_005325.2:p.Leu1587Phe | hom | hom | abs | abs | Uncertain significance (24 April 2017) |
GEMIN8 chrX | rs145874697 | T = 0.000638 (169/264690, TOPMED) T = 0.000769 (141/183241, GnomAD_exome) T = 0.000987 (104/105340, ALFA) | NM_001042480.1:c.514G > A NP_001035945.1:p.Val172Met | hom | hom | het | abs | Not reported |
POLE chr12 | rs5745066 | T = 0.018814 (5004/265972, ALFA) T = 0.014164 (1986/140212, GnomAD) T = 0.0201 (90/4480, Estonian) | NM_006231.3:c.6418G > A NP_006222.2:p.Glu2140Lys | hom | hom | abs | het | Benign/ Likely benign (8 December 2020) |
XK chrX | rs2230148 | T = 0.169863 (44961/264690, TOPMED) T = 0.167078 (17326/103700, GnomAD) T = 0.17009 (3524/20718, ALFA) | NM_021083.3:c.*89A > T | hom | hom | het | abs | Not reported |
RAD51C chr17 | rs28363317 | G = 0.005602 (1407/251152, GnomAD_exome) G = 0.006531 (916/140262, GnomAD) G = 0.0063 (28/4480, Estonian) | NM_058216.1:c.859A > G NP_478123.1:p.Thr287Ala | het | het | abs | abs | Benign/ Likely benign (1 February 2021) |