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) |
Gene names and missense mutations are shown in bold
According to NCBI; het, heterozygotic; hom, homozygotic; abs, absence. *Accessed on 16 November 2021