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Table 2 Detailed information of the clinically relevant variants identified in the family

From: Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants

GeneStatusVariationsMAF (GnomAD)ClinVarLOVDSIFTPoly-Phen2Mutat tasterACMGdSNP ID
USH2AHETM1: c.923_924dupGCCA
p. His308Glnfs*16
0.0000568 (16 alleles, 0 Hom)P (ID: 48615)P___5 (P)rs397518043
USH2AHETM2: c.1000C>T
p.Arg334Trp
0.0000531 (15 alleles, 0 Hom)P/LP (ID: 228411)P___5 (P)rs397517963
USH2AHETM3: c.2276G>T
p.Cys759Phe
0.0009677 (273 alleles, 0 Hom)P/LP (ID: 2356)P/LP___4 (LP)rs80338902
USH2AHETM4: c.12560G>A
p. Arg4187His
0.0000213 (6 alleles, 0 Hom)N.R.N.R.D
100%
B (0.066)SNP3 (VUS)rs147304271
PDZD7HETM5: c.1543C>T
p.Gln515*
0.0000134 (2 alleles, 0 Hom)N.R.N.R.D
100%
_DC5 (P)rs979094623
ADGRV1HETM6: c.13165_13166
insTGGAA
CTCCAGG
AGGG
p.Gly4360Glufs*10
_N.R.N.R._PD (0.999)DC4 (LP)_
  1. Reference sequences used: USH2A NM_206933, PDZD7 NM_024895 and ADGRV1 NM_032119
  2. B bening, D damaging, DC disease causing, Hom homozygous, ID identifier, L.P. likely pathogenic, N.R. not reported, P pathogenic, PD probably damaging, SNP single nucleotide polymorphism, VUS variant of unknown significance