DEL chr7:72,846,244-74,187,855
CNV summary
Our verdict is Pathogenic. Variant got ACMG score 1.45.
CNV loss of the region 7:72,846,244-74,187,855 (1.3 mb), is localized in (7)(q11.23). The region contains protein-coding and important regions. There is complete overlap with established HI region(s): dbVar:nssv15137072, dbVar:nssv15167740 (and 21 more). Among those, regions with breakpoints not laying inside the transcripts: morbid:DNAJC30, morbid:ELN (and 2 more). There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50 (and 16 more) in the affected region.
Genes
TODOClinGen
TODOACMG Results
Pathogenicity Level: Pathogenic
Score: 1.45
Criteria:
- LOSS_1A : 0 pointsRule : Contains protein-coding or other known functionally important elements.Details:The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072.
- LOSS_2A : 1 pointsRule : Complete overlap of a known pathogenic Loss SV.Details:There is complete overlap with established HI region(s): dbVar:nssv15137072, dbVar:nssv15167740, dbVar:nssv17955650, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15770120, dbVar:nssv15147201, dbVar:nssv15140244, dbVar:nssv15130169, dbVar:nssv15128343, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv16208140, HI3:ELN, dbVar:nssv17971140, dbVar:nssv16213814, dbVar:nssv18791887, morbid:FKBP6, dbVar:nssv18786274, dbVar:nssv17172746, dbVar:nssv15128578, dbVar:nssv16214480. Among those, regions with breakpoints not laying inside the transcripts: morbid:DNAJC30, morbid:ELN, HI3:ELN, morbid:FKBP6.
- LOSS_3B : 0.45 pointsRule : 25–34 genesDetails:There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H
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{ "cnvChange": { "chr": "7", "start": 72846244, "end": 74187855, "svType": "DEL" }, "annotations": { "chr": "7", "start": 72846244, "end": 74187855, "svType": "DEL", "length": 1341611, "geneGroups": [ "Nucleoporins", "Tripartite motif family|Ring finger proteins", "Speedy/RINGO cell cycle regulator family", "NOP2/Sun RNA methyltransferase family", "FKBP prolyl isomerases", "CD molecules|G protein-coupled receptors, Class F frizzled", "PHD finger proteins|Bromodomain containing|B-WICH chromatin-remodelling complex subunits", "BAF complex", "WD repeat domain containing", "Basic helix-loop-helix proteins", "ESCRT-I", "DNAJ (HSP40) heat shock proteins", "Ribosomal biogenesis factors|7BS DNA/RNA methyltransferases", "Syntaxins", "Abhydrolase domain containing", "Claudins", "7BS orphan methyltransferases", "LIM domain containing|PDZ domain containing|LIMK/TESK kinase family", "RNA binding motif containing|MicroRNA protein coding host genes" ], "cytobandString": "(7)(q11.23)", "overlappedGenes": [ { "id": "NM_022170.2", "chr": "7", "start": 74174356, "end": 74197096, "regionType": "GENE", "overlapType": "FIVE_UTR_WITH_CDS", "coveredFraction": 0.1072961373390558, "hgncId": 12741, "geneSummaryLongCarrier": { "symbol": "EIF4H", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000265753.13", "maneSelectRefSeqId": "NM_022170.2", "lof_pLI": 0.97545, "lof_oe_ci_upper": 0.508, "decipherHi": 0.2178, "geneGroup": "RNA binding motif containing|MicroRNA protein coding host genes" }, "overlappedGenePart": { "cdsBasesLost": 247, "cdsBasesSize": 747, "cdsFractionLost": 0.33065595716198126, "exonsBasesLost": 275, "exonsBasesSize": 2563, "exonsFractionLost": 0.1072961373390558, "lostExons": 2, "lostExonsRanks": [ 0, 1 ], "readingFrameDestroyed": true, "overlapType": "FIVE_UTR_WITH_CDS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_002314.4", "chr": "7", "start": 74083804, "end": 74122525, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 6613, "geneSummaryLongCarrier": { "symbol": "LIMK1", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000336180.7", "maneSelectRefSeqId": "NM_002314.4", "lof_pLI": 1, "lof_oe_ci_upper": 0.338, "decipherHi": 0.1966, "clingenHi": "NO_EVIDENCE_AVAILABLE", "clingenTs": "NO_EVIDENCE_AVAILABLE", "geneGroup": "LIM domain containing|PDZ domain containing|LIMK/TESK kinase family" }, "overlappedGenePart": { "cdsBasesLost": 1944, "cdsBasesSize": 1944, "cdsFractionLost": 1, "exonsBasesLost": 3355, "exonsBasesSize": 3355, "exonsFractionLost": 1, "lostExons": 16, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false }, "triploinsufficiencyType": "NO_EVIDENCE_AVAILABLE", "haploinsufficiencyType": "NO_EVIDENCE_AVAILABLE" }, { "id": "NM_000501.4", "chr": "7", "start": 74028173, "end": 74069907, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 3327, "geneSummaryLongCarrier": { "inheritances": [ "AD" ], "diseaseAssociations": [ { "classification": "DEFINITIVE", "diseaseName": "supravalvular aortic stenosis", "diseaseId": "MONDO:0008504", "inheritanceMode": null, "source": "GENCC" }, { "classification": "STRONG", "diseaseName": "cutis laxa, autosomal dominant 1", "diseaseId": "MONDO:0007411", "inheritanceMode": null, "source": "GENCC" }, { "classification": "STRONG", "diseaseName": "cutis laxa, autosomal dominant 1", "diseaseId": "MONDO:0007411", "inheritanceMode": null, "source": "GENCC" }, { "classification": "STRONG", "diseaseName": "cutis laxa, autosomal dominant 1", "diseaseId": "MONDO:0007411", "inheritanceMode": null, "source": "GENCC" }, { "classification": "DEFINITIVE", "diseaseName": "supravalvular aortic stenosis", "diseaseId": "MONDO:0008504", "inheritanceMode": null, "source": "GENCC" }, { "classification": "DEFINITIVE", "diseaseName": "cutis laxa, autosomal dominant 1", "diseaseId": "MONDO:0007411", "inheritanceMode": null, "source": "GENCC" }, { "classification": "SUPPORTIVE", "diseaseName": "supravalvular aortic stenosis", "diseaseId": "MONDO:0008504", "inheritanceMode": null, "source": "GENCC" }, { "classification": "SUPPORTIVE", "diseaseName": "autosomal dominant cutis laxa", "diseaseId": "MONDO:0019571", "inheritanceMode": null, "source": "GENCC" }, { "classification": "STRONG", "diseaseName": "cutis laxa, autosomal dominant 1", "diseaseId": "MONDO:0007411", "inheritanceMode": null, "source": "GENCC" }, { "classification": "STRONG", "diseaseName": "supravalvular aortic stenosis", "diseaseId": "MONDO:0008504", "inheritanceMode": null, "source": "GENCC" } ], "symbol": "ELN", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000252034.12", "maneSelectRefSeqId": "NM_000501.4", "lof_pLI": 7.2698e-10, "lof_oe_ci_upper": 0.697, "decipherHi": 0.0862, "clingenHi": "SUFFICIENT_EVIDENCE", "clingenHiDisease": "MONDO:0008504", "clingenTs": "NO_EVIDENCE_AVAILABLE" }, "overlappedGenePart": { "cdsBasesLost": 2175, "cdsBasesSize": 2175, "cdsFractionLost": 1, "exonsBasesLost": 3397, "exonsBasesSize": 3397, "exonsFractionLost": 1, "lostExons": 33, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 118, "escapeNmd": false }, "phenotypeHi": "MONDO:0008504", "triploinsufficiencyType": "NO_EVIDENCE_AVAILABLE", "haploinsufficiencyType": "SUFFICIENT_EVIDENCE" }, { "id": "NM_182504.4", "chr": "7", "start": 73861159, "end": 73865890, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 23018, "geneSummaryLongCarrier": { "symbol": "TMEM270", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000320531.3", "maneSelectRefSeqId": "NM_182504.4", "lof_pLI": 4.0928e-11, "lof_oe_ci_upper": 1.393 }, "overlappedGenePart": { "cdsBasesLost": 798, "cdsBasesSize": 798, "cdsFractionLost": 1, "exonsBasesLost": 851, "exonsBasesSize": 851, "exonsFractionLost": 1, "lostExons": 3, "lostExonsRanks": [ 0, 1, 2 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_152559.3", "chr": "7", "start": 73834590, "end": 73842516, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 19068, "geneSummaryLongCarrier": { "symbol": "METTL27", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000297873.9", "maneSelectRefSeqId": "NM_152559.3", "lof_pLI": 1.7608e-12, "lof_oe_ci_upper": 1.718, "geneGroup": "7BS orphan methyltransferases" }, "overlappedGenePart": { "cdsBasesLost": 738, "cdsBasesSize": 738, "cdsFractionLost": 1, "exonsBasesLost": 922, "exonsBasesSize": 922, "exonsFractionLost": 1, "lostExons": 6, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_001305.5", "chr": "7", "start": 73830996, "end": 73832690, "regionType": "GENE", "overlapType": "FIVE_UTR_WITH_CDS", "coveredFraction": 1, "hgncId": 2046, "geneSummaryLongCarrier": { "symbol": "CLDN4", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000340958.4", "maneSelectRefSeqId": "NM_001305.5", "lof_pLI": 0.00012713, "lof_oe_ci_upper": 1.44, "decipherHi": 0.2372, "geneGroup": "Claudins" }, "overlappedGenePart": { "cdsBasesLost": 630, "cdsBasesSize": 630, "cdsFractionLost": 1, "exonsBasesLost": 1695, "exonsBasesSize": 1695, "exonsFractionLost": 1, "lostExons": 1, "lostExonsRanks": [ 0 ], "readingFrameDestroyed": false, "overlapType": "FIVE_UTR_WITH_CDS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_001306.4", "chr": "7", "start": 73768997, "end": 73770270, "regionType": "GENE", "overlapType": "FIVE_UTR_WITH_CDS", "coveredFraction": 1, "hgncId": 2045, "geneSummaryLongCarrier": { "symbol": "CLDN3", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000395145.3", "maneSelectRefSeqId": "NM_001306.4", "lof_pLI": 0.45321, "lof_oe_ci_upper": 0.75, "decipherHi": 0.3346, "geneGroup": "Claudins" }, "overlappedGenePart": { "cdsBasesLost": 663, "cdsBasesSize": 663, "cdsFractionLost": 1, "exonsBasesLost": 1274, "exonsBasesSize": 1274, "exonsFractionLost": 1, "lostExons": 1, "lostExonsRanks": [ 0 ], "readingFrameDestroyed": false, "overlapType": "FIVE_UTR_WITH_CDS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_148912.4", "chr": "7", "start": 73736094, "end": 73738802, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 16407, "geneSummaryLongCarrier": { "symbol": "ABHD11", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000222800.8", "maneSelectRefSeqId": "NM_148912.4", "lof_pLI": 1.8683e-8, "lof_oe_ci_upper": 1.195, "decipherHi": 0.7655, "geneGroup": "Abhydrolase domain containing" }, "overlappedGenePart": { "cdsBasesLost": 921, "cdsBasesSize": 921, "cdsFractionLost": 1, "exonsBasesLost": 1418, "exonsBasesSize": 1418, "exonsFractionLost": 1, "lostExons": 6, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_004603.4", "chr": "7", "start": 73699210, "end": 73719669, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 11433, "geneSummaryLongCarrier": { "symbol": "STX1A", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000222812.8", "maneSelectRefSeqId": "NM_004603.4", "lof_pLI": 0.99999, "lof_oe_ci_upper": 0.258, "decipherHi": 0.2282, "geneGroup": "Syntaxins" }, "overlappedGenePart": { "cdsBasesLost": 867, "cdsBasesSize": 867, "cdsFractionLost": 1, "exonsBasesLost": 2102, "exonsBasesSize": 2102, "exonsFractionLost": 1, "lostExons": 10, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 6, "escapeNmd": false } }, { "id": "NM_017528.5", "chr": "7", "start": 73683597, "end": 73698212, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 16405, "geneSummaryLongCarrier": { "symbol": "BUD23", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000265758.7", "maneSelectRefSeqId": "NM_017528.5", "lof_pLI": 1.8804e-8, "lof_oe_ci_upper": 0.917, "geneGroup": "Ribosomal biogenesis factors|7BS DNA/RNA methyltransferases" }, "overlappedGenePart": { "cdsBasesLost": 846, "cdsBasesSize": 846, "cdsFractionLost": 1, "exonsBasesLost": 1201, "exonsBasesSize": 1201, "exonsFractionLost": 1, 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"source": "GENCC" } ], "symbol": "DNAJC30", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000395176.3", "maneSelectRefSeqId": "NM_032317.3", "lof_pLI": 5.8209e-7, "lof_oe_ci_upper": 1.485, "decipherHi": 0.8016, "geneGroup": "DNAJ (HSP40) heat shock proteins" }, "overlappedGenePart": { "cdsBasesLost": 681, "cdsBasesSize": 681, "cdsFractionLost": 1, "exonsBasesLost": 2536, "exonsBasesSize": 2536, "exonsFractionLost": 1, "lostExons": 1, "lostExonsRanks": [ 0 ], "readingFrameDestroyed": false, "overlapType": "FIVE_UTR_WITH_CDS", "numberOfPLpVariantsCovered": 3, "escapeNmd": false } }, { "id": "NM_001077621.2", "chr": "7", "start": 73667831, "end": 73672110, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 18287, "geneSummaryLongCarrier": { "symbol": "VPS37D", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000324941.5", "maneSelectRefSeqId": "NM_001077621.2", "lof_pLI": 0.26255, "lof_oe_ci_upper": 0.987, "decipherHi": 0.6411, "geneGroup": "ESCRT-I" }, "overlappedGenePart": { "cdsBasesLost": 756, "cdsBasesSize": 756, "cdsFractionLost": 1, "exonsBasesLost": 1618, "exonsBasesSize": 1618, "exonsFractionLost": 1, "lostExons": 4, "lostExonsRanks": [ 0, 1, 2, 3 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_032951.3", "chr": "7", "start": 73593202, "end": 73624522, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 12744, "geneSummaryLongCarrier": { "symbol": "MLXIPL", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000313375.8", "maneSelectRefSeqId": "NM_032951.3", "lof_pLI": 1.1896e-11, "lof_oe_ci_upper": 0.885, "decipherHi": 0.3645, "geneGroup": "Basic helix-loop-helix proteins" }, "overlappedGenePart": { "cdsBasesLost": 2559, "cdsBasesSize": 2559, "cdsFractionLost": 1, "exonsBasesLost": 3252, "exonsBasesSize": 3252, 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"FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_001707.4", "chr": "7", "start": 73536356, "end": 73557690, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 1005, "geneSummaryLongCarrier": { "symbol": "BCL7B", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000223368.7", "maneSelectRefSeqId": "NM_001707.4", "lof_pLI": 0.023124, "lof_oe_ci_upper": 0.868, "decipherHi": 0.2863, "geneGroup": "BAF complex" }, "overlappedGenePart": { "cdsBasesLost": 609, "cdsBasesSize": 609, "cdsFractionLost": 1, "exonsBasesLost": 1663, "exonsBasesSize": 1663, "exonsFractionLost": 1, "lostExons": 6, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": false } }, { "id": "NM_032408.4", "chr": "7", "start": 73440406, "end": 73522293, "regionType": "GENE", "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "coveredFraction": 1, "hgncId": 961, "geneSummaryLongCarrier": { "inheritances": [ "AD" ], "diseaseAssociations": [ { "classification": "LIMITED", "diseaseName": "autism spectrum disorder", "diseaseId": "MONDO:0005258", "inheritanceMode": null, "source": "GENCC" } ], "symbol": "BAZ1B", "proteinCoding": true, "maneSelectEnsemblId": "ENST00000339594.9", "maneSelectRefSeqId": "NM_032408.4", "lof_pLI": 1, "lof_oe_ci_upper": 0.201, "decipherHi": 0.2374, "geneGroup": "PHD finger proteins|Bromodomain containing|B-WICH chromatin-remodelling complex subunits" }, "overlappedGenePart": { "cdsBasesLost": 4452, "cdsBasesSize": 4452, "cdsFractionLost": 1, "exonsBasesLost": 6115, "exonsBasesSize": 6115, "exonsFractionLost": 1, "lostExons": 20, "lostExonsRanks": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 ], "readingFrameDestroyed": false, "overlapType": "FULL_LAST_EXON_WITH_PREVIOUS_EXONS", "numberOfPLpVariantsCovered": 0, "escapeNmd": 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"oth_AN": 1482, "oth_AC": 0, "oth_AF": 0, "sas_AN": 4068, "sas_AC": 0, "sas_AF": 0 } }, { "chr": "7", "start": 74186250, "end": 74186813, "gnomadSvEntry": { "afr_AN": 33656, "afr_AC": 7, "afr_AF": 0.000208, "ami_AN": 842, "ami_AC": 0, "ami_AF": 0, "amr_AN": 12542, "amr_AC": 1, "amr_AF": 0.00008, "asj_AN": 3172, "asj_AC": 0, "asj_AF": 0, "eas_AN": 4032, "eas_AC": 1, "eas_AF": 0.000248, "fin_AN": 6460, "fin_AC": 2, "fin_AF": 0.00031, "mid_AN": 64, "mid_AC": 0, "mid_AF": 0, "nfe_AN": 58758, "nfe_AC": 3, "nfe_AF": 0.000051, "oth_AN": 1552, "oth_AC": 0, "oth_AF": 0, "sas_AN": 4368, "sas_AC": 0, "sas_AF": 0 } } ] }, "acmg": { "position": { "chr": "7", "start": 72846244, "end": 74187855 }, "criteria": [ { "criterium": "LOSS_1A", "points": 0 }, { "criterium": "LOSS_2A", "points": 1 }, { "criterium": "LOSS_3B", "points": 0.45 } ], "criteriaReports": [ { "criterium": "LOSS_1A", "report": "The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072. " }, { "criterium": "LOSS_2A", "report": "There is complete overlap with established HI region(s): dbVar:nssv15137072, dbVar:nssv15167740, dbVar:nssv17955650, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15770120, dbVar:nssv15147201, dbVar:nssv15140244, dbVar:nssv15130169, dbVar:nssv15128343, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv16208140, HI3:ELN, dbVar:nssv17971140, dbVar:nssv16213814, dbVar:nssv18791887, morbid:FKBP6, dbVar:nssv18786274, dbVar:nssv17172746, dbVar:nssv15128578, dbVar:nssv16214480. Among those, regions with breakpoints not laying inside the transcripts: morbid:DNAJC30, morbid:ELN, HI3:ELN, morbid:FKBP6. " }, { "criterium": "LOSS_3B", "report": "There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H" } ], "criteriaData": [ { "criterium": "LOSS_1A", "report": "The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072. ", "met": true, "points": 0 }, { "criterium": "LOSS_2A", "report": "There is complete overlap with established HI region(s): dbVar:nssv15137072, dbVar:nssv15167740, dbVar:nssv17955650, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15770120, dbVar:nssv15147201, dbVar:nssv15140244, dbVar:nssv15130169, dbVar:nssv15128343, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv16208140, HI3:ELN, dbVar:nssv17971140, dbVar:nssv16213814, dbVar:nssv18791887, morbid:FKBP6, dbVar:nssv18786274, dbVar:nssv17172746, dbVar:nssv15128578, dbVar:nssv16214480. Among those, regions with breakpoints not laying inside the transcripts: morbid:DNAJC30, morbid:ELN, HI3:ELN, morbid:FKBP6. ", "met": true, "points": 1 }, { "criterium": "LOSS_3B", "report": "There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H", "met": true, "points": 0.45 } ], "report": "CNV loss of the region 7:72,846,244-74,187,855 (1.3 mb), is localized in (7)(q11.23). The region contains protein-coding and important regions. There is complete overlap with established HI region(s): dbVar:nssv15137072, dbVar:nssv15167740 (and 21 more). Among those, regions with breakpoints not laying inside the transcripts: morbid:DNAJC30, morbid:ELN (and 2 more). There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50 (and 16 more) in the affected region. ", "pathogenicityLevel": "Pathogenic", "score": 1.45, "svType": "DEL", "phenotype": null } }