Table 1.
Five homozygous rare variants in five novel candidate genes identified in four RP probands
| Genes | Chromosome | Reference | Patient | Variant | Nucleotide | Amino acid | Expression & interaction§ |
Allele frequency in gnomAD |
Allele frequency of other LoF variants |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| position | transcript | ID | number | change | change | Retina | IRD genes | All | EA | control | gnomAD | |
| ENSA | chr01: 150599935 | NM_207168 | ZOCRP0009 | M1 | c.191delG | p.Gly64Alafs*2 | Ninth | OFD1 | 1/251460 | 1/18394 | 2/9456 | 22/282912 |
| DACT2 | chr06: 168710973 | NM_214462 | ZOCRP0156 | M2 | c.533C>A | p.Ser178* | Second | NA | NA | NA | 4/9456 | 144/282912 |
| EXTL2 | chr01: 101343065 | NM_001439 | ZOCRP0156 | M3 | c.400C>T | p.Arg134* | Highest | NA | 3/247450 | 3/18342 | 2/9456 | 37/282912 |
| DDR1 | chr06: 30864446 | NM_001202523 | ZOCRP0830 | M4 | c.1616dupT | p.Pro540Alafs*15 | Fifth | CCT2, BBS10 | NA | NA | 0/9456 | 178/282912 |
| CCDC188 | chr22: 20136745 | NM_001243537 | ZOCRP0559 | M5 | c.163C>T | p.Arg55* | NA | NA | NA | NA | 0/9456 | 63/282912 |
Notes: EA, East Asian; gnomAD, genome aggregation database; IRD, inherited retinal degeneration; LoF, loss-of-function; M, mutation; NA, not available.
§Information based on GeneCards where expression in retina ranked by SAGE.
None of these variants was present in Exome Variant Server or 1000 Genomes.
No homozygous LoF variants in these five genes were found in the gnomAD database.