Table 2 Genes mapping to the duplicated genomic region
Sample | Locus | dnCNV Coordinates(GRCh38) | dnCNV type | OMIM disease genes (associated trait MIM#) mapping in duplicated region | Number of genes(pLi > 0.9) | Total number of genes overlapping duplication region | ACMG classification evidence* | ACMG classification |
|---|---|---|---|---|---|---|---|---|
BAB9637 | 4q31.22q31.23 | chr4:147494740-148399180 | DUP | EDNRA (#616367, AD); NR3C2 (#177735, AD) | 2 | 10 | 1A, 2J, 3A, 4D | VUS |
BAB9637 | 5q35.2q35.3 | chr5:176449583-177376826 | DUP | SNCB (#127750, AD); NSD1 (#117550, AD) | 3 | 23 | 1A, 2A | Pathogenic |
BAB9637 | 6p24.2p24.1 | chr6:11481309-12522879 | DUP | EDN1 (#612798, AD; #615706, AR) | 1 | 10 | 1A, 3A, 4D | VUS |
BAB9637 | 10q26.13q26.2 | chr10:124920875-125841697 | DUP | UROS (#263700, AR); MMP21 (#616749, AR) | 1 | 16 | 1A, 3A, 4D | VUS |
BAB9637 | 12q13.2q13.3 | chr12:55986511-56885590 | DUP | MIP (#615274, AD), ERBB3 (#133180, AD; #607598, AR),SMARCC2 (#618362, AD), RPS26 (#613309, AD), SLC39A5 (#615946, AD), SUOX (#272300, AR), STAT2 (#618886, AR; #616636, AR) | 8 | 40 | 1A, 2H, 3B, 4B | VUS |
BAB9637 | 13q33.3q34 | chr13:109406834-110341135 | DUP | COL4A1 (#180000, AD; #611773, AD; #175780, AD; #618564, AD), COL4A2 (#614483, AD), IRS2 (#125853, AD) | 1 | 8 | 1A, 3A, 4D | VUS |
BAB9637 | 14q21.1 | chr14:40568596-41479705 | DUP | 0 | 0 | 1B | VUS | |
BAB9637 | 21q21.3 | chr21:28158347-29192300 | DUP | 1 | 12 | 1A, 3A, 4D | VUS | |
BAB3097 | 1p36.22p36.13 | chr1:10115497-16283149 | DUP | KIF1B (#118210, AD; #171300, AD; #256700), PEX14 (#614887, AR), TARDBP (#612069, AD), MASP2 (#613791, AR), MTOR (#616638, AD), UBIAD1 (#121800, AD), MAD2L2 (#617243, AR), MTHFR (#236250, AR), CLCN6 (#619173, AD), NPPA (#612201, AD; #615745, AR), PLOD1 (#225400, AR), MFN2 (#609260, AD; #617087, AR; #601152, AD), VPS13D (#607317, AR), CELA2A (#618620, AD), SPEN (#619312, AD), CLCNKA (#613090, DR), CLCNKB (#607364, AR; #613090, DR), EPHA2 (#116600, AD) | 13 | 167 | 1A, 3C, 4C | Likely Pathogenic |
BAB3097 | 3q13.33q21.1 | chr3:122157406-123113479 | DUP | CASR (#239200, AD/AR; #601198, AD; #145980, AD), CSTA (#607936, AR) | 19 | 2 | 1A, 3A, 4D | VUS |
BAB3097 | 5p12 | chr5:44375961-44815730 | DUP | FGF10 (#180920, AD; #149730, AD) | 0 | 2 | 1A, 2J, 3A, 4D | VUS |
BAB3097 | 5q33.3q34 | chr5:158887731-164722046 | DUP | IL12B (#614890, AR), GABRB2 (#617829, AD), GABRA1 (#615744, AD), GABRG2 (#618396, AD; #607681, AD) | 5 | 42 | 1A, 3A, 4D | VUS |
BAB3097 | 9p13.3 | chr9:33492358-34725916 | TRP | UBAP1 (#618418, AD), MYORG (#618317, AR), DNAI1 (#244400, AR), SIGMAR1 (#614373, AR; #605726, AR), GALT (#230400, AR), IL11RA (#614188, AR) | 4 | 53 | 1A, 3C, 4D | VUS |
BAB3097 | 17p12p11.2 | chr17:11915997-17892664 | DUP | DNAH9 (#618300, AR), MYOCD (#618719, AD), ELAC2 (#615440, AR), COX10 (#619046, AR), PMP22 (#139393, AD; #118220, AD; #118300 AD; #145900, AD; #162500, AD; #180800, AD), TTC19 (#615157, AR), PIGL (#280000, AR), TNFRSF13B (#240500, AD/AR), FLCN (#135150, AD; #173600, AD), RAI1 (#182290, AD), SREBF1 (#619016, AD; #158310, AD) | 7 | 110 | 1A, 2A | Pathogenic |
BAB3097 | 22q13.31p13.32 | chr22:47979382-48288823 | DUP | 0 | 1 | 1A, 3A, 4D | VUS | |
mCNV3/BAB9484 | 1p31.3p31.1 | chr1:66885559-77949895 | DUP | SLC35D1 (#269250, AR), WLS (#619648, AR), RPE65 (#204100, AR; #613794, AR; #618697, AD), CTH (#219500, AR), TNNI3K (#616117, AD), ACADM (#201450, AR), PIGK (#618879, AR), NEXN (#613122, AD; #613876, AD) | 9 | 108 | 1A, 3C, 4D | VUS |
mCNV3/BAB9484 | 1q42.2q42.3 | chr1:233450789-235471180 | DUP | COA6 (#616501, AR), IRF2BP2 (#617765, AD), GGPS1 (#619518, AR), TBCE (#617207, AR; #241410, AR; #244460, AR), B3GALNT2 (#615181, AR) | 1 | 35 | 1A, 3B, 4D | VUS |
mCNV3/BAB9484 | 2p13.3 | chr2:69512973-71153026 | DUP | ASPRV1 (#146750, AD), TIA1 (#619133, AD; #604454, AD/AR), FIGLA (#612310, AD), ATP6V1B1 (#267300, AR), MCEE (#251120, AR) | 2 | 44 | 1A, 3B, 4D | VUS |
mCNV3/BAB9484 | 3q26.32 | chr3:176661565-177473432 | DUP | TBL1XR1 (#616944, AD; #602342, AD) | 1 | 8 | 1A, 2A, 3A, 4C | Likely Pathogenic |
mCNV3/BAB9484 | 9q22.2 | chr9:89241202-90787598 | DUP | SECISBP2 (#609698, AR) | 2 | 38 | 1A, 3B, 4D | VUS |
mCNV3/BAB9484 | 11p12p11.2 | chr11:42871836-44852545 | DUP | EXT2 (#133701, AD; #616682, AR), ALX4 (#613451, AR; #609597, AD; #615529, AD) | 2 | 25 | 1A, 2H, 3B, 4D | VUS |
mCNV3/BAB9484 | 16q22.2 | chr16:71219688-71768356 | DUP | HYDIN (#608647, AR), TAT (#276600, AR), AP1G1 (#619467, AD) | 1 | 16 | 1A, 3A, 4D | VUS |
mCNV3/BAB9484 | 20q13.33 | chr20:61800345-63644611 | DUP | OSBPL2 (#616340, AD), GATA5 (#617912, AD/AR), COL9A3 (#600969, AD), SLC17A9 (#616063, AD), CHRNA4 (#600513, AD), KCNQ2 (#613720, AD; #121200, AD), EEF1A2 (#616409, AD; #616393, AD) | 4 | 15 | 1A, 3A, 4D | VUS |