CRX (Cone-rod homeobox protein) variants and mutations
CRX (also known as Cone-rod homeobox protein) is a human protein-coding gene encoding a cone-rod homeobox protein. It activates photoreceptor-specific gene programs required for development and maintenance of rods and cones. Pathogenic variants can cause cone-rod dystrophy, Leber congenital amaurosis, or dominant retinitis pigmentosa depending on the molecular mechanism. This analysis covers 737 CRX variants and mutations. Of these, 80% have computational variant effect predictions. Disease context includes Leber congenital amaurosis, cone-rod dystrophy 2, and Leber congenital amaurosis 7. Example CRX variants include M2T, A3P, and A3S.
Variant analysis overview
- Gene: CRX
- Protein: Cone-rod homeobox protein
- UniProt accession: O43186
- Organism: Homo sapiens
- Variants analyzed: 737
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 436 unspecified-consequence records; 124 missense variants; 154 synonymous variants; 4 stop-gained variants; 8 frameshift variants; 6 in-frame deletions; 2 splice-region variants; 1 stop lost; 1 in-frame insertions; 3 substitution
- Prediction scores: 593 variants have prediction scores (80% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Leber congenital amaurosis, cone-rod dystrophy 2, Leber congenital amaurosis 7, retinitis pigmentosa, Cone rod dystrophy, cone-rod dystrophy, Retinal dystrophy, autosomal dominant retinitis pigmentosa, neurodegenerative disease, benign concentric annular macular dystrophy, Stargardt disease, Leber congenital amaurosis 1.
Protein structure and variant hotspots
- Experimental data: 55 protein positions have experimental scores. Source: CRX Homeobox domain domainome 1.0.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable CRX variants
Examples include M2T, A3P, A3S, A3T, A3V, A3E, A3A, Y4C. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M2T (p.Met2Thr), gnomAD 19-47834448-T-C, REVEL 0.84, CADD 24.80
- A3P (p.Ala3Pro), gnomAD rs1229606751, REVEL 0.43, CADD 25.00
- A3S (p.Ala3Ser), gnomAD rs1229606751
- A3T (p.Ala3Thr), gnomAD rs1229606751
- A3V (p.Ala3Val), rs762715327, ClinGen CA9544358, cosmic curated COSV99032, ClinVar RCV001057955, REVEL 0.48, CADD 23.40, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2; Retinal dystrophy
- A3E (p.Ala3Glu), gnomAD 19-47834451-C-A, REVEL 0.44, CADD 23.20
- A3A (p.Ala3Ala), rs140766502, gnomAD 19-47834452-G-A, CADD 7.42
- Y4C (p.Tyr4Cys), rs1211313175, ClinGen CA406628612, ClinVar RCV001323352, ClinVar RCV004692502, REVEL 0.81, CADD 26.90, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7; not provided
- Y4H (p.Tyr4His), ESP rs150122798, ExAC rs150122798, TOPMed rs150122798, gnomAD rs150122798, REVEL 0.74, CADD 26.10
- Y4N (p.Tyr4Asn), ESP rs150122798, ExAC rs150122798, TOPMed rs150122798, gnomAD rs150122798, REVEL 0.83, CADD 26.20
- M5I (p.Met5Ile), ExAC rs776868419, TOPMed rs776868419, gnomAD rs776868419, REVEL 0.21, CADD 19.80
- M5T (p.Met5Thr), gnomAD rs1458143033, REVEL 0.49, CADD 23.00
- M5V (p.Met5Val), ESP rs145337312, ExAC rs145337312, TOPMed rs145337312, gnomAD rs145337312, REVEL 0.30, CADD 22.20
- N6S (p.Asn6Ser), gnomAD rs1230960052, REVEL 0.37, CADD 23.00
- N6N (p.Asn6Asn), gnomAD 19-47834461-C-T, CADD 8.96
- P7L (p.Pro7Leu), rs558522333, ClinGen CA9544364, ClinVar RCV001990192, ClinVar RCV004816816, REVEL 0.46, CADD 24.80, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- P7T (p.Pro7Thr), ExAC rs762329875
- P7S (p.Pro7Ser), gnomAD 19-47834462-C-T, REVEL 0.41, CADD 24.60
- P7Q (p.Pro7Gln), gnomAD 19-47834463-C-A, REVEL 0.37, CADD 21.90
- P7P (p.Pro7Pro), rs772745666, gnomAD 19-47834464-G-A, CADD 9.56
- G8R (p.Gly8Arg), rs146240568, ClinGen CA9544366, ClinVar RCV001345352, ClinVar RCV005540401, REVEL 0.32, CADD 23.80, Conflicting interpretations, Leber congenital amaurosis 7; Cone-rod dystrophy 2; Inborn genetic diseases
- G8E (p.Gly8Glu), gnomAD 19-47834466-G-A, REVEL 0.39, CADD 23.70
- G8G (p.Gly8Gly), gnomAD 19-47834467-G-T, CADD 9.27
- P9H (p.Pro9His), cosmic curated COSV99704, ExAC rs766003111, gnomAD rs766003111, REVEL 0.58, CADD 24.20
- P9S (p.Pro9Ser), rs2123738269, ClinGen CA406628746, ClinVar RCV002000899, Ensembl rs2123738269, REVEL 0.60, CADD 24.60, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- P9P (p.Pro9Pro), gnomAD 19-47834470-C-T, CADD 8.61
- H10D (p.His10Asp), rs139340178, ClinGen CA9544368, ClinVar RCV000280624, ClinVar RCV000401704, REVEL 0.49, CADD 22.70, Conflicting interpretations, Retinal dystrophy; Leber congenital amaurosis 7; Cone-rod dystrophy 2
- H10P (p.His10Pro), ExAC rs754630141, gnomAD rs754630141, REVEL 0.51, CADD 21.90, Uncertain significance
- H10R (p.His10Arg), rs754630141, ClinGen CA9544369, ClinVar RCV001260906, ExAC rs754630141, REVEL 0.30, CADD 16.10, Uncertain significance, Usher syndrome
- H10Q (p.His10Gln), gnomAD 19-47834473-C-A, REVEL 0.45, CADD 22.20
- H10H (p.His10His), rs1327438189, gnomAD 19-47834473-C-T, CADD 8.34
- Y11C (p.Tyr11Cys), gnomAD 19-47834475-A-G, REVEL 0.80, CADD 26.10
- S12F (p.Ser12Phe), ExAC rs767285003, gnomAD rs767285003, REVEL 0.34, CADD 22.80
- S12P (p.Ser12Pro), Ensembl rs1968092201
- V13A (p.Val13Ala), ExAC rs756039866, TOPMed rs756039866, gnomAD rs756039866, REVEL 0.33, CADD 23.10
- V13F (p.Val13Phe), NCI-TCGA Cosmic COSV5575, NCI-TCGA Cosmic COSV5576, cosmic curated COSV55760, Variant assessed as somatic; moderate impact.
- V13L (p.Val13Leu), rs752458888, ClinGen CA9544371, ClinVar RCV003804293, ClinVar RCV005435308, REVEL 0.28, CADD 22.30, Conflicting interpretations, not specified; Leber congenital amaurosis 7; Cone-rod dystrophy 2
- N14K (p.Asn14Lys), rs774344094, ClinGen CA9544375, ClinVar RCV002038047, ExAC rs774344094, REVEL 0.38, CADD 22.50, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- N14S (p.Asn14Ser), ExAC rs777613986, gnomAD rs777613986, REVEL 0.40, CADD 22.50
- N14N (p.Asn14Asn), rs774344094, gnomAD 19-47834485-C-T, CADD 5.55
- A15D (p.Ala15Asp), gnomAD rs1318083411, REVEL 0.27, CADD 22.20
- A15P (p.Ala15Pro), rs559181643, ClinGen CA406628824, ClinVar RCV001075819, ClinVar RCV002554773, REVEL 0.29, CADD 20.90, Uncertain significance, Retinal dystrophy; Cone-rod dystrophy 2; Leber congenital amaurosis 7
- A15T (p.Ala15Thr), rs559181643, ClinGen CA9544376, NCI-TCGA Cosmic COSV5575, cosmic curated COSV55759, REVEL 0.25, CADD 19.40, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- A15V (p.Ala15Val), gnomAD rs1318083411, REVEL 0.28, CADD 22.20
- A15A (p.Ala15Ala), rs955358343, gnomAD 19-47834488-C-G, CADD 7.54
- L16* (p.Leu16Ter), gnomAD 19-47834490-T-A, CADD 38.00
- L16L (p.Leu16Leu), rs1030462247, gnomAD 19-47834491-G-A, CADD 7.65
- A17V (p.Ala17Val), gnomAD 19-47834493-C-T, REVEL 0.29, CADD 22.40
- L18V (p.Leu18Val), gnomAD 19-47834495-C-G, REVEL 0.35, CADD 16.00
- L18L (p.Leu18Leu), rs747167744, gnomAD 19-47834495-C-T, CADD 4.77
- S19I (p.Ser19Ile), Ensembl rs2123738310
- S19C (p.Ser19Cys), gnomAD 19-47834498-A-T, REVEL 0.30, CADD 22.60
- G20V (p.Gly20Val), gnomAD 19-47834502-G-T, REVEL 0.65, CADD 24.00
- G20G (p.Gly20Gly), rs769017861, gnomAD 19-47834503-C-T, CADD 9.19
- G20S (p.Gly20Ser), rs1254989456, gnomAD 19-47839340-G-A, CADD 9.66
- P21S (p.Pro21Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P21P (p.Pro21Pro), gnomAD 19-47834506-C-G, CADD 8.40
- S22V (p.Ser22Val), rs775167405, gnomAD 19-47834502-GC-G, CADD 23.40
- D24N (p.Asp24Asn), NCI-TCGA Cosmic COSV5575, cosmic curated COSV55759, Variant assessed as somatic; moderate impact.
- L25M (p.Leu25Met), gnomAD rs1210601065, REVEL 0.33, CADD 21.20
- L25P (p.Leu25Pro), gnomAD rs1236725891, REVEL 0.78, CADD 27.10, Benign, Cone-rod dystrophy 2
- M26I (p.Met26Ile), rs886054544, ClinGen CA10652151, ClinVar RCV000298080, ClinVar RCV000341362, REVEL 0.22, CADD 22.80, Uncertain significance, Cone-rod dystrophy 2; Inborn genetic diseases; Leber congenital amaurosis 7
- M26V (p.Met26Val), gnomAD 19-47834519-A-G, REVEL 0.26, CADD 22.70
- p.His27 Ala29del, gnomAD 19-47834521-GCACC, CADD 18.70
- Q28R (p.Gln28Arg), rs781577708, ClinGen CA9544380, ClinVar RCV001370444, ClinVar RCV004980395, REVEL 0.18, CADD 21.30, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2; Inborn genetic diseases
- Q28Q (p.Gln28Gln), rs1196202479, gnomAD 19-47834527-G-A, CADD 4.95
- A29T (p.Ala29Thr), rs2514250194, ClinGen CA406629091, ClinVar RCV003079373, REVEL 0.27, CADD 17.80, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- A29V (p.Ala29Val), TOPMed rs1190997138
- V30E (p.Val30Glu), rs2514250200, ClinGen CA406629111, ClinVar RCV003054109, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- V30L (p.Val30Leu), gnomAD 19-47834531-G-C, REVEL 0.52, CADD 22.60
- V30A (p.Val30Ala), gnomAD 19-47834532-T-C, REVEL 0.55, CADD 22.10
- V30V (p.Val30Val), rs1968093050, gnomAD 19-47834533-G-A, CADD 8.69
- P31S (p.Pro31Ser), cosmic curated COSV10728, TOPMed rs1453222875, gnomAD rs1453222875
- P31T (p.Pro31Thr), TOPMed rs1453222875, gnomAD rs1453222875, REVEL 0.23, CADD 22.40
- P31A (p.Pro31Ala), gnomAD 19-47834532-T-TC, CADD 25.90
- P31P (p.Pro31Pro), gnomAD 19-47834536-C-A, CADD 9.22
- Y32H (p.Tyr32His), gnomAD 19-47834537-T-C, REVEL 0.70, CADD 26.40
- Y32* (p.Tyr32Ter), gnomAD 19-47834539-C-A, CADD 36.00
- Y32Y (p.Tyr32Tyr), rs748498259, gnomAD 19-47834539-C-T, CADD 5.60
- P33H (p.Pro33His), gnomAD 19-47834540-C-CAT, CADD 29.50
- P33Q (p.Pro33Gln), gnomAD 19-47834541-C-A, REVEL 0.52, CADD 26.90
- P33P (p.Pro33Pro), rs770311577, gnomAD 19-47834542-A-G, CADD 0.60
- S34I (p.Ser34Ile), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, Variant assessed as somatic; moderate impact.
- S34N (p.Ser34Asn), ExAC rs748529936, gnomAD rs748529936
- S34R (p.Ser34Arg), 1000Genomes rs139778328, ESP rs139778328, ExAC rs139778328, TOPMed rs139778328, REVEL 0.34, CADD 8.47, Benign
- S34S (p.Ser34Ser), rs139778328, gnomAD 19-47836244-C-T, CADD 0.66
- A35D (p.Ala35Asp), TOPMed rs1360808512, gnomAD rs1360808512, REVEL 0.30, CADD 18.70
- A35T (p.Ala35Thr), rs778203784, NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, ExAC rs778203784, REVEL 0.28, CADD 12.30, Variant assessed as somatic; moderate impact.
- A35A (p.Ala35Ala), rs886054545, gnomAD 19-47836247-C-T, CADD 1.60
- P36H (p.Pro36His), rs193920917, ClinGen CA174095, NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, AlphaMissense 0.31, MetaLR 0.89, Uncertain significance, Prostate cancer
- P36S (p.Pro36Ser), rs2514252109, ClinGen CA406629378, ClinVar RCV002305159, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- P36P (p.Pro36Pro), rs1968116015, gnomAD 19-47836250-C-T, CADD 0.85
- R37T (p.Arg37Thr), gnomAD rs1968116056, REVEL 0.78, CADD 25.30
- R37Q (p.Arg37Gln), gnomAD 19-47836245-G-GC, CADD 23.20
- R37R (p.Arg37Arg), rs2123739849, gnomAD 19-47836251-A-C, CADD 7.57
- R37K (p.Arg37Lys), gnomAD 19-47836252-G-A, REVEL 0.68, CADD 25.10
- K38R (p.Lys38Arg), TOPMed rs1968116093, Uncertain significance, Cone-rod dystrophy 2
- Q39K (p.Gln39Lys), gnomAD 19-47836257-C-A, REVEL 0.75, CADD 24.90
- Q39* (p.Gln39Ter), gnomAD 19-47836257-C-T, CADD 43.00
- R40P (p.Arg40Pro), rs771450991, ClinGen CA406629427, ClinVar RCV002885697, AlphaMissense 0.98, MetaLR 0.95, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- R40Q (p.Arg40Gln), rs771450991, ClinGen CA9544402, ClinVar RCV000504788, ClinVar RCV001857203, REVEL 0.87, AlphaMissense 0.98, Pathogenic/Likely pathogenic, Cone-rod dystrophy 2; Leber congenital amaurosis 7; not provided
- R40W (p.Arg40Trp), rs749738655, ClinGen CA9544401, NCI-TCGA Cosmic COSV5575, cosmic curated COSV55759, REVEL 0.94, CADD 28.90, Pathogenic/Likely pathogenic, not provided; Retinal dystrophy; Leber congenital amaurosis 7
- R40R (p.Arg40Arg), rs749738655, gnomAD 19-47836260-C-A, CADD 11.50
- R41Q (p.Arg41Gln), rs61748436, ClinGen CA118791, NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, REVEL 0.93, CADD 28.50, Pathogenic/Likely pathogenic, Inborn genetic diseases; Retinal dystrophy; Leber congenital amaurosis 7
- R41W (p.Arg41Trp), rs104894672, ClinGen CA118790, cosmic curated COSV55758, ClinVar RCV000007843, REVEL 0.95, CADD 25.60, Pathogenic, Cone-rod dystrophy 2; Leber congenital amaurosis 7; Retinal dystrophy
- R41G (p.Arg41Gly), gnomAD 19-47836260-CG-C, CADD 32.00
- R41R (p.Arg41Arg), gnomAD 19-47836263-C-A, CADD 9.88
- R41P (p.Arg41Pro), gnomAD 19-47836264-G-C, REVEL 0.98, CADD 28.70
- E42D (p.Glu42Asp), ExAC rs759088105, gnomAD rs759088105, REVEL 0.57, CADD 23.00, Uncertain significance, in LCA7
- E42K (p.Glu42Lys), rs863224863, ClinGen CA278974, NCI-TCGA Cosmic COSV5575, cosmic curated COSV55759, AlphaMissense 0.98, MetaLR 0.82, Conflicting interpretations, Cone-rod dystrophy 2; Leber congenital amaurosis 7; Retinal dystrophy
- E42G (p.Glu42Gly), gnomAD 19-47836267-A-G, REVEL 0.77, CADD 30.00
- E42E (p.Glu42Glu), rs759088105, gnomAD 19-47836268-G-A, CADD 6.70
- E42Q (p.Glu42Gln), rs1968161064, gnomAD 19-47839337-G-C, CADD 9.87
- R43C (p.Arg43Cys), rs1437021651, ClinGen CA406629451, cosmic curated COSV55756, ClinVar RCV000787585, REVEL 0.90, CADD 26.80, Pathogenic, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- R43H (p.Arg43His), rs771736389, ClinGen CA9544404, NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, REVEL 0.98, CADD 28.40, Pathogenic/Likely pathogenic, Cone-rod dystrophy 2; Leber congenital amaurosis 7; not provided
- R43L (p.Arg43Leu), rs771736389, ClinGen CA406629455, ClinVar RCV002029275, ExAC rs771736389, REVEL 0.97, CADD 28.10, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- R43S (p.Arg43Ser), rs1437021651, ClinGen CA406629448, NCI-TCGA Cosmic COSV5575, NCI-TCGA Cosmic COSV9970, REVEL 0.95, CADD 24.90, Likely pathogenic, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- T44I (p.Thr44Ile), ExAC rs760519102, TOPMed rs760519102, gnomAD rs760519102, REVEL 0.96, CADD 25.00, Uncertain significance, Inborn genetic diseases
- T44T (p.Thr44Thr), rs763733046, gnomAD 19-47836274-C-A, CADD 9.29
- T45A (p.Thr45Ala), rs2514252159, ClinGen CA406629469, ClinVar RCV003112649, NCI-TCGA Cosmic COSV5575, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- T45I (p.Thr45Ile), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T45T (p.Thr45Thr), gnomAD 19-47836277-C-A, CADD 9.22
- F46F (p.Phe46Phe), rs199607129, gnomAD 19-47836280-C-T, CADD 10.20
- T47A (p.Thr47Ala), TOPMed rs1939392843, Uncertain significance
- T47I (p.Thr47Ile), rs1203670123, ClinGen CA406629500, ClinVar RCV001972092, ClinVar RCV003264299, REVEL 0.96, CADD 24.80, Uncertain significance, Inborn genetic diseases; Leber congenital amaurosis 7; Cone-rod dystrophy 2
- T47P (p.Thr47Pro), rs1939392843, ClinGen CA406629492, ClinVar RCV001198956, TOPMed rs1939392843, AlphaMissense 0.66, MetaLR 0.93, Uncertain significance, Retinitis pigmentosa
- T47N (p.Thr47Asn), gnomAD 19-47836282-C-A, REVEL 0.89, CADD 24.30
- T47T (p.Thr47Thr), gnomAD 19-47836283-C-A, CADD 2.85
- R48P (p.Arg48Pro), ExAC rs765302774, TOPMed rs765302774, gnomAD rs765302774, REVEL 0.79, CADD 26.50, Uncertain significance
- R48Q (p.Arg48Gln), rs765302774, ClinGen CA9544410, NCI-TCGA Cosmic COSV5575, cosmic curated COSV55756, REVEL 0.70, CADD 29.90, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- R48W (p.Arg48Trp), rs761797993, ClinGen CA9544409, NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, REVEL 0.74, CADD 23.10, Uncertain significance, Retinal dystrophy; Leber congenital amaurosis 7; Cone-rod dystrophy 2
- R48R (p.Arg48Arg), gnomAD 19-47836284-C-A, CADD 7.14
- S49G (p.Ser49Gly), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, REVEL 0.36, CADD 22.50, Variant assessed as somatic; moderate impact.
- S49N (p.Ser49Asn), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99704, Variant assessed as somatic; moderate impact.
- S49R (p.Ser49Arg), ExAC rs751665561, gnomAD rs751665561, REVEL 0.44, CADD 23.60, Uncertain significance, Retinal dystrophy
- Q50H (p.Gln50His), ExAC rs755068966, TOPMed rs755068966, gnomAD rs755068966, REVEL 0.81, CADD 21.00, Uncertain significance, not provided
- L51L (p.Leu51Leu), rs1441890796, gnomAD 19-47836293-C-T, CADD 9.14
- L51Q (p.Leu51Gln), gnomAD 19-47836294-T-A, REVEL 0.95, CADD 26.60
- E52* (p.Glu52Ter), NCI-TCGA Cosmic COSV5575, cosmic curated COSV55757, Variant assessed as somatic; high impact.
- E53G (p.Glu53Gly), TOPMed rs967929101, gnomAD rs967929101, REVEL 0.62, CADD 31.00, Likely pathogenic, Retinal dystrophy
- E53K (p.Glu53Lys), NCI-TCGA Cosmic COSV5575, cosmic curated COSV55757, Variant assessed as somatic; moderate impact.
- E53E (p.Glu53Glu), rs767773596, gnomAD 19-47836301-G-A, CADD 9.09
- E55G (p.Glu55Gly), gnomAD rs1452594516, REVEL 0.97, CADD 32.00
- E55K (p.Glu55Lys), Ensembl rs1968117023
- E55E (p.Glu55Glu), rs1968117124, gnomAD 19-47836307-G-A, CADD 7.80
- A56T (p.Ala56Thr), rs61748437, ClinGen CA227612, ClinVar RCV000085991, ClinVar RCV001369855, REVEL 0.72, CADD 23.50, Conflicting interpretations, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- A56S (p.Ala56Ser), gnomAD 19-47836308-G-T, REVEL 0.35, CADD 16.20
- A56A (p.Ala56Ala), gnomAD 19-47836310-A-G, CADD 3.89
- L57V (p.Leu57Val), gnomAD 19-47836311-C-G, REVEL 0.64, CADD 19.90
- L57P (p.Leu57Pro), gnomAD 19-47836312-T-C, REVEL 0.88, CADD 25.60
- F58C (p.Phe58Cys), ExAC rs756371710, gnomAD rs756371710, REVEL 0.95, CADD 26.50
- A59S (p.Ala59Ser), TOPMed rs1405463340, gnomAD rs1405463340, REVEL 0.41, CADD 20.50
- A59T (p.Ala59Thr), TOPMed rs1405463340, gnomAD rs1405463340
- A59A (p.Ala59Ala), rs1325090607, gnomAD 19-47836319-C-T, CADD 8.93
- K60E (p.Lys60Glu), ESP rs370973957, ExAC rs370973957, gnomAD rs370973957, REVEL 0.73, CADD 25.30
- K60M (p.Lys60Met), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T61I (p.Thr61Ile), rs1599985527, ClinGen CA406629648, ClinVar RCV002033569, TOPMed rs1599985527, REVEL 0.92, CADD 24.30, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- T61S (p.Thr61Ser), TOPMed rs1599985527, Uncertain significance
- Q62L (p.Gln62Leu), gnomAD 19-47836327-A-T, REVEL 0.59, CADD 23.60
- Y63D (p.Tyr63Asp), Ensembl rs759987549
- P64A (p.Pro64Ala), gnomAD rs1368658678, REVEL 0.95, CADD 24.10
- P64L (p.Pro64Leu), TOPMed rs1722653625
- P64T (p.Pro64Thr), gnomAD rs1368658678
- P64S (p.Pro64Ser), gnomAD 19-47836332-C-T, REVEL 0.95, CADD 24.60
- D65H (p.Asp65His), rs527236062, ClinGen CA270027, ClinVar RCV000132604, ClinVar RCV003888547, REVEL 0.97, CADD 26.60, Likely pathogenic, Retinal dystrophy
- D65D (p.Asp65Asp), rs757731373, gnomAD 19-47836337-C-T, CADD 4.07
- V66F (p.Val66Phe), rs61748438, ClinGen CA406629694, ClinVar RCV002001280, 1000Genomes rs61748438, REVEL 0.68, CADD 24.70, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- V66I (p.Val66Ile), rs61748438, ClinGen CA227614, cosmic curated COSV55759, ClinVar RCV000085992, REVEL 0.56, CADD 15.80, Benign/Likely benign, Retinal dystrophy; not specified; Leber congenital amaurosis 7
- V66V (p.Val66Val), gnomAD 19-47836340-C-T, CADD 5.60
- Y67S (p.Tyr67Ser), gnomAD 19-47836342-A-C, REVEL 0.66, CADD 24.80
- A68T (p.Ala68Thr), Ensembl rs1968117786, REVEL 0.49, CADD 24.70
- A68V (p.Ala68Val), rs145649717, ClinGen CA9544417, ClinVar RCV001361102, 1000Genomes rs145649717, REVEL 0.43, CADD 22.70, Likely benign, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- A68A (p.Ala68Ala), gnomAD 19-47836346-C-T, CADD 6.52
- R69C (p.Arg69Cys), rs771551785, ClinGen CA9544418, cosmic curated COSV55759, ClinVar RCV000678552, REVEL 0.87, CADD 25.00, Pathogenic/Likely pathogenic, not provided; Cone-rod dystrophy 2; Leber congenital amaurosis 7
- R69G (p.Arg69Gly), rs771551785, ClinGen CA406629722, ClinVar RCV003056494, REVEL 0.83, CADD 25.70, Uncertain significance, Cone-rod dystrophy 2; Leber congenital amaurosis 7
- R69H (p.Arg69His), rs775073228, ClinGen CA9544419, cosmic curated COSV55758, ClinVar RCV001093247, REVEL 0.82, CADD 24.70, Pathogenic/Likely pathogenic, Retinal dystrophy; not provided; Cone-rod dystrophy 2
- E70V (p.Glu70Val), ExAC rs746588900, gnomAD rs746588900, REVEL 0.80, CADD 23.50
- E71K (p.Glu71Lys), rs1206525536, ClinGen CA406629740, cosmic curated COSV10728, ClinVar RCV002637767, REVEL 0.78, CADD 28.40, Uncertain significance, Leber congenital amaurosis 7; Cone-rod dystrophy 2
- E71E (p.Glu71Glu), rs185420673, gnomAD 19-47836355-G-A, CADD 7.67
- V72A (p.Val72Ala), ExAC rs776533441, gnomAD rs776533441, REVEL 0.83, CADD 26.20
Public CRX analysis runs
- CRX analysis run — CRX (737 variants) — completed 2026-08-22