Table 3.
Genetic data of identified variants
| dbSNP | Nucleotide change | Protein change | Variant type | Predicted effect | ACMG classification (applied criteriaA) | Count in cohort (n of patients/families) | First report |
|---|---|---|---|---|---|---|---|
| ABHD12 (NM_001042472.3) | |||||||
| c.728G > A | p.(Trp243*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| ADGRV1 (NM_032119.4) | |||||||
| c.(17019 + 1_17020-1)_(17856 + 1_17857-1)dup | CNV | Exon 79–83 duplication | Likely pathogenic | 3 / 2 | This study | ||
| rs757696771 | c.17668_17669del | p.(Met5890Valfs*10) | Indel | Frameshift | Pathogenic (PVS1, PS4, PM2, PP5) | 3 / 3 | PMID: 21569298 |
| rs746618021 | c.2864C > A | p.(Ser955*) | SNV | Nonsense | Pathogenic (PVS1, PS4, PM2, PP5) | 1 / 1 | PMID: 22147658 |
| rs397517429 | c.2870dup | p.(Asn957Lysfs*10) | Indel | Frameshift | Pathogenic (PVS1, PM2, PP5) | 1 / 1 | This study |
| c.6515C > G | p.(Ser2172*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| c.7336del | p.(Glu2446Asnfs*21) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| c.9484G > T | p.(Glu3162*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 2 / 1 | This study | |
| c.17669del | p.(Met5890Valfs*10) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 5 / 4 | This study | |
| c.8832del | p.(Gly2945Valfs*2) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| ARL2BP (NM_012106.4) | |||||||
| rs199830550 | c.207 + 1G > A | p.? | SNV | Splicing | Pathogenic (PVS1, PM2, PM3, PP5) | 2 / 2 | PMID: 28041643 |
| ARSG (NM_001267727.2) | |||||||
| rs751461705 | c.1326del | p.(Ser443Alafs*12) | Indel | Frameshift | Pathogenic (PVS1, PS3, PM2, PM3, PP5) | 4 / 3 | PMID: 33300174 |
| rs141748845 | c.253 T > C | p.(Ser85Pro) | SNV | Missense | Pathogenic (PM2, PM3, PP3, PP5) | 1 / 1 | PMID: 33300174 |
| rs1244718647 | c.338G > A | p.(Gly113Asp) | SNV | Missense | Pathogenic (PM2, PM3 PP3, PP5) | 1 / 1 | PMID: 33300174 |
| BBS1 (NM_024649.5) | |||||||
| rs113624356 | c.1169 T > G | p.(Met390Arg) | SNV | Missense | Pathogenic (PS3, PM2, PM3, PP1, PP3, PP5) | 10 / 9 | PMID: 12118255 |
| rs1014835928 | c.1318C > T | p.(Arg440*) | SNV | Nonsense | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID: 12677556 |
| c.863 T > G | p.(Leu288Arg) | SNV | Missense | Likely pathogenic (PM2, PM3, PP3, PP4) | 1 / 1 | This study | |
| rs1490351829 | c.118del | p.(Cys40Alafs*2) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID: 27032803 |
| rs121917777 | c.1645G > T | p.(Glu549*) | SNV | Nonsense | Pathogenic (PVS1, PM2, PM3, PP5) | 3 / 2 | PMID: 12118255 |
| c.17C > G | p.(Ser6*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| BBS2 (NM_031885.5) | |||||||
| rs1368647604 | c.402del | p.(Ala136Argfs*65) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 2 / 1 | PMID: 15770229 |
| rs121908178 | c.943C > T | p.(Arg315Trp) | SNV | Missense | Likely pathogenic (PS3, PM1, PM2, PM3, PM5, PP3, PP5) | 2 / 1 | PMID: 11567139 |
| BBS10 (NM_024685.4) | |||||||
| rs1057517031 | c.1542del | p.(Asp515Ilefs*9) | Indel | Frameshift | Pathogenic (PVS1, PM2, PP5) | 3 / 1 | PMID: 16582908 |
| rs549625604 | c.271dup | p.(Cys91Leufs*15) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID: 10874630 |
| rs148374859 | c.273C > G | p.(Cys91Trp) | SNV? | Missense | Pathogenic (PS3, PM2, PM3, PP5) | 2 / 2 | PMID: 16582908 |
| c.1677del | p.(Tyr559*) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID: 16582908 | |
| CDH23 (NM_022124.6) | |||||||
| rs1385831846 | c.3579 + 2 T > C | p.? | SNV | Splicing | Pathogenic (PVS1, PS4, PM2, PP5) | 1 / 1 | PMID: 11138009 |
| rs1306728898 | c.6319C > T | p.(Arg2107*) | SNV | Nonsense | Pathogenic (PVS1, PM2, PP5) | 1 / 1 | PMID: 11090341 |
| rs111033247 | c.6049 + 1G > A | p.? | SNV | Splicing | Pathogenic (PVS1, PS4, PM2, PP5) | 1 / 1 | PMID: 8894709 |
| c.753 + 2 T > A | p.? | SNV | Splicing | Likely Pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| CNNM4 (NM_020184.4) | |||||||
| rs74552543 | c.971 T > C | p.(Leu324Pro) | SNV | Missense | Pathogenic (PM2, PM3, PP3, PP5) | 1 / 1 | PMID: 19200527 |
| DNAJC21 (NM_001012339.3) | |||||||
| c.805C > T | p.(Gln269*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| MKKS (NM_170784.3) | |||||||
| rs768929313 | c.748G > A | p.(Gly250Arg) | SNV | Missense | Pathogenic (PM2, PM3, PM5, PP3, PP5) | 3 / 1 | PMID: 20142850 |
| MT-ATP6 | |||||||
| rs199476133 | m.8993 T > G | p.(Leu156Arg) | SNV | Missense | Pathogenic (PS2, PM3, PM5, PP3, PP5) | 2 / 1 | PMID: 2137962 |
| MYO7A (NM_000260.4) | |||||||
| c.1529 T > C | p.(Ile510Thr) | SNV | Missense | Likely pathogenic (PM1, PM2, PM3, PP3) | 1 / 1 | This study | |
| rs111033214 | c.3508G > A | p.(Glu1170Lys) | SNV | Missense | Pathogenic (PS4, PM2 PM5, PP3, PP5) | 5 / 3 | PMID: 10425080 |
| rs111033187 | c.397dup | p.(His133Profs*7) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 7 / 4 | PMID: 21569298 |
| rs751769391 | c.4489G > C | p.(Gly1497Arg) | SNV | Missense | Pathogenic (PM2, PM5, PP3, PP5) | 3 / 3 | PMID: 27460420 |
| c.5510 T > A | p.(Leu1837His) | SNV | Missense | Pathogenic (PM2, PM5, PP3, PP5) | 4 / 4 | PMID: 36909829 | |
| c.5743-15_5746del | p.(Ala1915fs) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| rs1591514873 | c.6439-1G > A | p.? | SNV | Splicing | Pathogenic (PVS1, PM2, PP5) | 3 / 2 | PMID: 16199547 |
| rs111033285 | c.999 T > G | p.(Tyr333*) | SNV | Nonsense | Pathogenic (PVS1, PS4, PM2, PP5) | 1 / 1 | PMID: 8900236 |
| c.1929dup | p.(Pro644Alafs*67) | Indel | Frameshift | Pathogenic (PVS1, PM2, PP5) | 2 / 1 | PMID: 36909829 | |
| rs1173853484 | c.6026C > A | p.(Ala2009Asp) | SNV | Missense | Likely pathogenic (PP3, PP5, PM1, PM2, PM5) | 1 / 1 | PMID: 27460420 |
| NPHP1 (NM_001128178.3) | |||||||
| c.2065_2074del | p.(Thr689Leufs*37) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 2 / 2 | This study | |
| NPHP4 (NM_015102.5) | |||||||
| rs370946873 | c.2956G > A | p.(Gly986Arg) | SNV | Missense | VUS (PM2, PP3) | 1 / 1 | PMID: 36909829 |
| NRL (NM_001354768.3) | |||||||
| rs774348345 | c.74G > A | p.(Arg25Gln) | SNV | Missense | VUS (PM2, PP2) | 1 / 1 | This study |
| PANK2 (NM_001386393.1) | |||||||
| rs779815683 | c.1268G > T | p.(Cys423Phe) | SNV | Missense | VUS (PM1, PM2, PP2, PP3) | 1 / 1 | This study |
| rs137852959 | c.1561G > A | p.(Gly521Arg) | SNV | Missense | Pathogenic (PS3, PM2, PM3, PP1, PP2, PP3, PP5) | 1 / 1 | PMID: 11479594 |
| rs754521581 | c.1070G > C | p.(Arg357Pro) | SNV | Missense | Likely pathogenic (PM1, PM2, PM3, PM5, PP2, PP5) | 1 / 1 | PMID: 28680084 |
| PCDH15 (NM_001384140.1) | |||||||
| c.(2220 + 1_2221-1)_(3122 + 1_3123-1)dup | CNV | Exon 19–23 duplication | Likely pathogenic | 1 / 1 | PMID: 20538994 | ||
| SDCCAG8 (NM_006642.5) | |||||||
| rs768207230 | c.397G > T | p.(Glu133*) | SNV | Nonsense | Pathogenic (PVS1, PM2, PM3, PP5) | 2 / 2 | This study |
| SLC7A14 (NM_020949.3) | |||||||
| rs116040996 | c.821C > T | p.(Thr274IIe) | SNV | Missense | VUS (PP3, PM2) | 1 / 1 | This study |
| TRAF3IP1 (NM_015650.4) | |||||||
| rs778376663 | c.916-4A > G | p.? | SNV | Splicing | Likely pathogenic (PP3, PM2, PM3) | 2 / 1 | PMID: 36909829 |
| TTC8 (NM_001288781.1) | |||||||
| c.647G > A | p.(Trp216*) | SNV | Missense | Likely pathogenic (PVS1, PM2, PP5) | 1 / 1 | This study | |
| c.(?_681-1)_(879 + 1_?)del | CNV | Exon 9–10 deletion | Likely pathogenic | 1 / 1 | |||
| USH1G (NM_173477.5) | |||||||
| c.183 T > A | p.(Cys61*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| USH2A (NM_206933.4) | |||||||
| rs750228923 | c.1214del | p.(Asn405Ilefs*3) | Indel | Frameshift | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID:16098008 |
| c.12294 + 1559_14133 + 8144del | CNV | Exon 63–64 deletion | Likely pathogenic | 1 / 1 | PMID: 28041643 | ||
| rs998302546 | c.14134-3169A > G | p.? | SNV | Splicing | Likely pathogenic (PM2, PM3, PP5) | 2 / 1 | PMID: 29196752 |
| c.14423G > A | p.(Cys4808Tyr) | SNV | Missense | VUS (PM1, PM2, PM3) | 1 / 1 | PMID: 36909829 | |
| c.1879C > T | p.(Gln627*) | SNV | Nonsense | Likely pathogenic (PVS1, PM2) | 1 / 1 | This study | |
| rs111033334 | c.2209C > T | p.(Arg737*) | SNV | Nonsense | Pathogenic (PVS1, PM2, PM3, PP5) | 1 / 1 | PMID: 17296898 |
| rs80338902 | c.2276G > T | p.(Cys759Phe) | SNV | Missense | Pathogenic (PS4, PM1, PM2, PM3, PP1, PP3, PP4, PP5) | 1 / 1 | PMID: 1968399 |
| c.(7300 + 1_7301-1)_(9371 + 1_9372-1)del | CNV | Exon 38–47 deletion | Likely pathogenic | 3 / 2 | |||
| rs202175091 | c.10712C > T | p.(Thr3571Met) | SNV | Missense | Pathogenic (PM1, PM2, PM3, PM5, PP1, PP5) | 1 / 1 | PMID: 17085681 |
| rs527236139 | c.11156G > A | p.(Arg3719His) | SNV | Missense | Pathogenic (PP1, PP5, PM2, PM3) | 2 / 2 | PMID: 20507924 |
| rs397517994 | c.14911C > T | p.(Arg4971*) | SNV | Nonsense | Pathogenic (PVS1, PP5, PM2, PM3) | 2 / 1 | PMID: 10729113 |
| rs758660532 | c.15089C > A | p.(Ser5030*) | SNV | Nonsense | Pathogenic (PVS1, PP5, PM2, PM3) | 2 / 1 | PMID: 10729113 |
| rs80338903 | c.2299del | p.(Glu767Serfs*21) | Indel | Frameshift | Pathogenic (PVS1, PP1, PP5, PM2, PM3) | 2 / 2 | PMID: 9624053 |
| rs1052375050 | c.2302 T > C | p.(Cys768Arg) | SNV | Missense | Likely pathogenic (PP3, PM2) | 1 / 1 | PMID: 36909829 |
| rs759433119 | c.2809 + 1G > A | p.? | SNV | Splicing | Pathogenic (PVS1, PP5, PM2, PM3) | 2 / 1 | PMID: 10729113 |
| rs754374132 | c.5278del | p.(Asp1760Metfs*10) | Indel | Frameshift | Pathogenic (PVS1, PP5, PM2, PM3) | 1 / 1 | PMID: 10729113 |
| rs1571783742 | c.7932G > A | p.(Trp2644*) | SNV | Nonsense | Pathogenic (PVS1, PP5, PM2, PM3) | 2 / 2 | PMID: 10729113 |
| rs748465849 | c.907C > A | p.(Arg303Ser) | SNV | Missense | Pathogenic (PP5, PM2, PM3, PM5) | 3 / 3 | PMID: 14970843 |
| rs397518043 | c.920_923dup | p.(His308Glnfs*16) | Indel | Frameshift | Pathogenic (PVS1, PP5, PM2, PM3) | 5 / 5 | PMID: 18641288 |
| rs111033263 | c.9799 T > C | p.(Cys3267Arg) | SNV | Missense | Likely pathogenic (PP3, PP5,PM2, PM3, PM5) | 1 / 1 | PMID: 17085681 |
| c.9315del | p.(Val3106Trpfs*54) | Indel | Frameshift | Likely pathogenic (PVS1, PM2) | 1 / 1 | PMID: 36909829 | |
| rs150982499 | c.5039A > G | p.(Lys1680Arg) | SNV | Missense | VUS (PM1, PM2) | 1 / 1 | PMID: 28912962 |
| WDR19 (NM_025132.4) | |||||||
| rs1020915921 | c.2704-2A > C | p.? | SNV | Splicing | Pathogenic (PVS1, PP5, PM2) | 1 / 1 | PMID: 16199547 |
| rs387906980 | c.1649 T > C | p.(Leu550Ser) | SNV | Missense | Pathogenic (PP1, PP3, PP5, PM2, PM3) | 1 / 1 | PMID: 22019273 |
AEach ACMG pathogenicity criterion is weighted as very strong (PVS), strong (PS), moderate (PM), or supporting (PP)
dbSNP, single nucleotide polymorphism database; PMID, PubMed identifier; VUS, variant of uncertain significance