Table S4.
Variants from WGS analyses of the COPI complex genes
| Gene | Identifier | Alt. Ex | Variant | No. of families | No. of affected carriers | Med. AAO | No. of unaffected carriers | MAF (dbSNP) | MAF (WGS) |
| COPA | ENST00000368069 | nEx 33 | nAA 1,233 | ||||||
| rs57425682 | 6 | T146A | 14 | 20/29 | 73 | 2/6 | 0.003 | 0.007 | |
| 1:160278885 | 5 | 5′ splice | 1 | 2/2 | 72.5 | 0/0 | N/A | 0.0007 | |
| rs75190422 | 8 | 5′ splice | 6 | 8/10 | 65.5 | 0/1 | 0.001 | 0.003 | |
| 1:160303386 | 28 | 5′ splice | 1 | 3/4 | 75 | 0/0 | N/A | 0.001 | |
| 1:160283843 | 9 | R260C | 1 | 2/3 | 68 | 0/1 | N/A | 0.0007 | |
| COPB1 | ENST00000249923 | nEx 22 | nAA 953 | ||||||
| 11:14521151 | 1 | 3′ splice | 6 | 9/16 | 77 | 1/12 | N/A | 0.003 | |
| rs201467424 | 18 | V789I | 1 | 3/3 | 76 | 0/0 | N/A | 0.001 | |
| rs375670951 | 8 | 5′ splice | 1 | 3/3 | 76 | 0/0 | N/A | 0.001 | |
| 11:14520389 | 2 | D29Y | 1 | 2/2 | 76.5 | 0/0 | N/A | 0.0007 | |
| 11:14502548 | 9 | R351K | 1 | 2/3 | 78.5 | 0/2 | N/A | 0.0007 | |
| rs144780995 | 15 | P625S | 1 | 3/3 | 70.5 | 0/0 | N/A | 0.0007 | |
| COPG1 | ENST00000314797 | nEx 24 | nAA 874 | ||||||
| 3:128968592 | 1 | 5′ splice | 1 | 2/2 | 70.5 | 0/0 | N/A | 0.0007 | |
| COPG2 | ENST00000445977 | nEx 9 | nAA 246 | ||||||
| rs143820112 | 4 | 3′ splice | 1 | 2/2 | 64 | 0/0 | N/A | 0.0007 | |
| COPD | ENST00000264028 | nEx 10 | nAA 511 | ||||||
| rs78730658 | 3 | 5′ splice | 4 | 7/11 | 78 | 0/0 | 0.001 | 0.002 | |
| rs188303468 | 1 | 3′ splice | 2 | 3/5 | 70 | 0/2 | 0.005 | 0.001 | |
| rs138863361 | 2 | A6S | 2 | 3/5 | 70 | 0/2 | 0.005 | 0.001 | |
| COPE | ENST00000262812 | nEx 10 | nAA 308 | ||||||
| rs2231987 | 1 | S13C | 18 | 27/40 | 74 | 4/13 | 0.07 | 0.01 | |
| rs199731661 | 10 | 5′ splice | 6 | 6/11 | 72 | 2/7 | 0.003 | 0.02 | |
| rs141039416 | 3 | R96Q | 1 | 2/2 | 79 | 0/0 | N/A | 0.0007 | |
| rs34510432 | 3 | R85H | 1 | 2/3 | 66 | 0/0 | 0.005 | 0.0007 | |
| COPZ1 | ENST00000262061 | nEx 9 | nAA 177 | ||||||
| 12:54741793 | 7 | E136Q | 1 | 2/2 | 69 | 0/0 | N/A | 0.0007 | |
| COPZ2 | ENST00000006101 | nEx 10 | nAA 208 | ||||||
| rs115870363 | 6 | 3′ splice | 9 | 13/17 | 75 | 2/3 | 0.004 | 0.005 | |
| 17:46115120 | 2 | 6, frameshift | 1 | 2/2 | 87.5 | 0/0 | N/A | 0.001 | |
| 17:46115121 | 2 | W6R | 1 | 2/2 | 87.5 | 0/0 | N/A | 0.001 |
The variants resulting from the analyses of the nine COPI genes are listed above. Identifier: dbSNP (The Single Nucleotide Polymorphism Database) ID when available or the physical location of the variant in the genome (hg19 reference panel). Alt. Ex: exon affected by the variation. Variant: impact of the mutation. No. of families: number of families where at least one subject is a carrier. No. of affected carriers: ratio of the number of subjects showing the presence of the alternate allele/total number of affected patients in the carrier families. Med. AAO: median onset age of the AD patients. No. of unaffected carriers: ratio of the number of unaffected family members carrying the alternate allele/total number of unaffected in the carrier families. MAF (dbSNP) and MAF (WGS): frequency of the minor alternate allele in the reported study population. ENST, Ensembl Canonical Transcript ID for the gene of interest; N/A, not available; nAA, number of amino acids in the transcribed protein; nEx, number of exons in the gene transcript.