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[Preprint]. 2023 Dec 27:2023.12.22.23300468. [Version 1] doi: 10.1101/2023.12.22.23300468

Table 1. Non-coding candidate variants and putative target genes.

1Coding loss-of-function intolerance - https://doi.org/10.1038/s41586-020-2308-7; 2Coding dosage sensitivity - https://doi.org/10.1016/j.cell.2022.06.036; 3Non-coding mutational constraint (1 kb windows) - https://doi.org/10.1101/2022.03.20.485034; †Multi-hit gene; ††Multi-hit peak; †††non-coding deletion; *mean value across deleted interval; (Y) denotes established CCDD gene for stated phenotype; AD: autosomal dominant/de novo, ar(h): autosomal recessive homozygous, ar(ch): autosomal recessive compound heterozygous, I: intronic, P: promoter, D: distal, LoF: loss-of-function, GoF: gain-of-function.

CCDD Pedigree Inheritance Non-coding
variant(hg38)		 Peak Type Nearest gene Target gene Distance to
target (kb)		 Reporter ID Peak to gene r Peak to gene
FDR		 gnomAD allele
frequency		 Predicted
mechanism		 SAD Z-score Target gene
loeuf1 		Target gene
pHaplo2 		Target gene
pTriplo2 		Non-coding
Z-score3
CFEOM S25 AD chr10:129794079 TTGAG>T D EBF3 EBF3† (Y-DRS) 170 hs2776 0.24 2.90E-07 8.37E-05 LoF −11.77 0.15 1.00 1.00 3.10
MGJW S176 AD chr10:129884231 C>A I EBF3 EBF3† (Y-DRS) - hs2775 0.29 3.89E-10 4.88E-05 GoF 0.11 0.15 1.00 1.00 3.74
Ptosis S95 AD chr10:129944464 G>C I EBF3 EBF3† (Y-DRS) - hs2774 0.21 7.76E-06 - GoF 0.98 0.15 1.00 1.00 5.14
DRS S12 ar(h) chr11:72394626 C>G I CLPB PHOX2A (Y-CFEOM) 156 - 0.26 1.09E-08 1.41E-03 GoF 0.18 0.80 0.76 0.98 2.32
Ptosis S32 AD chr2:175005662 C>T†† P CHN1 CHN1 (Y-DRS) - - 0.48 1.31E-28 1.39E-04 LoF −0.38 0.57 0.41 0.72 2.59
CFEOM/DRS S251 AD chr2:175006051 GCTT>G†† P CHN1 CHN1 (Y-DRS) - - 0.48 1.31E-28 - GoF 2.29 0.57 0.41 0.72 2.08
DRS S230 AD chr20:40866929-40945626††† D TOP1 MAFB (Y-DRS) 256 hs2769 hs2770 0.23* 1.19E-05* - - - 0.40 0.94 1.00 2.19*
CFP S205 ar(ch) chr5:51172762 T>A D ISL1 ISL1 221 hs1321 0.74 1.36E-86 2.26E-03 LoF −0.41 0.23 0.95 0.85 −2.28
CFP S205 ar(ch) chr5:51172961 T>G D ISL1 ISL1 221 hs1321 0.74 1.36E-86 2.33E-03 LoF −0.12 0.23 0.95 0.85 −2.28
DRS S190, S238 ar(h) chr22:27493955-27497536††,††† D MN1 MN1 307 hs2757 - - 1.38E-04 - - 0.48 0.99 0.92 0.29*
DRS S191 ar(ch) chr17:1455690 G>A†† I CRK CRK - - - - - GoF 0.44 0.34 0.97 1.00 0.30
DRS S191 ar(ch) chr17:1456361 G>A†† P CRK CRK - - - - 1.51E-03 LoF −1.24 0.34 0.97 1.00 -
DRS S211 ar(ch) chr17:1455565 C>T†† I CRK CRK - - - - 1.19E-04 GoF 0.49 0.34 0.97 1.00 0.30
DRS S211 ar(ch) chr17:1456436G C>G†† P CRK CRK - - - - 3.77E-04 LoF −12.28 0.34 0.97 1.00 -
DRS S211 ar(ch) chr17:1456438 G>A†† P CRK CRK - - - - 3.77E-04 LoF −2.06 0.34 0.97 1.00 -
DRS WL AD chr17:48003752 A>C†† D CDK5RAP3 CDK5RAP3 22 hs2777 0.57 8.04E-43 - GoF 4.31 0.97 0.24 0.54 1.94
MBS S174 ar(ch) chr17:48003557 C>G†† D CDK5RAP3 CDK5RAP3 22 hs2777 0.57 8.04E-43 4.04E-03 LoF −0.15 0.97 0.24 0.54 1.94
MBS S174 ar(ch) chr17:48003826 C>T†† D CDK5RAP3 CDK5RAP3 22 hs2777 0.57 8.04E-43 9.42E-04 GoF 1.69 0.97 0.24 0.54 1.94
CFP S156 AD chr3:128459417G>C†† D DNAJB8 GATA2 7 - 0.28 6.08E-10 - LoF −4.88 0.34 0.98 0.87 -
CFP S180 AD chr3:128459454A>G†† D DNAJB8 GATA2 7 - 0.28 6.08E-10 3.95E-05 GoF 2.88 0.34 0.98 0.87 -
CFP S194 AD chr3:128459455G>A†† D DNAJB8 GATA2 7 - 0.28 6.08E-10 - GoF 11.40 0.34 0.98 0.87 -