7:72846244-74187855 DEL
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 over established HI gene(s): ELN. There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN (and 21 more). Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650 (and 6 more). ClinGen associates these changes with phenotype(s): MONDO:0008504. 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
ABHD11 BAZ1B BCL7B BUD23 CLDN3 CLDN4 DNAJC30 EIF4H ELN FKBP6 FZD9 LIMK1 METTL27 MLXIPL NSUN5 POM121 SPDYE10 SPDYE11 SPDYE8 SPDYE9 STX1A TBL2 TMEM270 TRIM50 TRIM74 VPS37DClinGen
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:nssv15129678.
- LOSS_2A : 1 pointsRule : Complete overlap of a known pathogenic Loss SV.Details:There is complete overlap with established HI gene(s): ELN. There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv17955650, dbVar:nssv18791887, dbVar:nssv15128578, dbVar:nssv17971140, dbVar:nssv15130169, dbVar:nssv16214480, dbVar:nssv15770120, dbVar:nssv17172746, dbVar:nssv15137072, dbVar:nssv15128343, dbVar:nssv18786274, HI3:ELN, dbVar:nssv15140244, morbid:FKBP6, dbVar:nssv15147201, dbVar:nssv16208140, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15167740. Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650, dbVar:nssv15137072, dbVar:nssv15128343, HI3:ELN, morbid:FKBP6, dbVar:nssv16208140, morbid:DNAJC30.
- 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
Genes affected
ABHD11 (whole gene)
Position: chr7-73736094-73738802
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.9e-8
Decipher HI: 0.77
pHaplo:
pTriplo:
BAZ1B (whole gene)
Position: chr7-73440406-73522293
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.0
Decipher HI: 0.24
pHaplo:
pTriplo:
BCL7B (whole gene)
Position: chr7-73536356-73557690
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.023
Decipher HI: 0.29
pHaplo:
pTriplo:
BUD23 (whole gene)
Position: chr7-73683597-73698212
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.9e-8
Decipher HI:
pHaplo:
pTriplo:
CLDN3 (whole gene)
Position: chr7-73768997-73770270
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.45
Decipher HI: 0.33
pHaplo:
pTriplo:
CLDN4 (whole gene)
Position: chr7-73830996-73832690
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.00013
Decipher HI: 0.24
pHaplo:
pTriplo:
DNAJC30 (whole gene)
Position: chr7-73680918-73683453
Region Type: GENE
Protein Coding: Yes
LoF pLI: 5.8e-7
Decipher HI: 0.80
pHaplo:
pTriplo:
EIF4H (overlap type is "five utr_with_cds". 33.07% of coding sequence and 10.73% of exons, reading frame is destroyed.)
Position: chr7-74174356-74197096
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.98
Decipher HI: 0.22
pHaplo:
pTriplo:
ELN (whole gene)
Position: chr7-74028173-74069907
Region Type: GENE
Protein Coding: Yes
clingenHi: SUFFICIENT_EVIDENCE
clingenHiDisease:MONDO:0008504
clingenTs: NO_EVIDENCE_AVAILABLE
LoF pLI: 7.3e-10
Decipher HI: 0.086
pHaplo:
pTriplo:
FKBP6 (whole gene)
Position: chr7-73328161-73358625
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.0000040
Decipher HI: 0.66
pHaplo:
pTriplo:
FZD9 (whole gene)
Position: chr7-73433778-73436120
Region Type: GENE
Protein Coding: Yes
LoF pLI: 5.8e-11
Decipher HI: 0.47
pHaplo:
pTriplo:
LIMK1 (whole gene)
Position: chr7-74083804-74122525
Region Type: GENE
Protein Coding: Yes
clingenHi: NO_EVIDENCE_AVAILABLE
clingenTs: NO_EVIDENCE_AVAILABLE
LoF pLI: 1.0
Decipher HI: 0.20
pHaplo:
pTriplo:
METTL27 (whole gene)
Position: chr7-73834590-73842516
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.8e-12
Decipher HI:
pHaplo:
pTriplo:
MLXIPL (whole gene)
Position: chr7-73593202-73624522
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.2e-11
Decipher HI: 0.36
pHaplo:
pTriplo:
NSUN5 (whole gene)
Position: chr7-73302516-73308826
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.1e-10
Decipher HI: 0.70
pHaplo:
pTriplo:
POM121 (whole gene)
Position: chr7-72925095-72948299
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.0023
Decipher HI: 0.87
pHaplo:
pTriplo:
SPDYE10 (whole gene)
Position: chr7-73104008-73155431
Region Type: GENE
Protein Coding: Yes
LoF pLI:
Decipher HI:
pHaplo:
pTriplo:
SPDYE11 (whole gene)
Position: chr7-73047862-73057911
Region Type: GENE
Protein Coding: Yes
LoF pLI:
Decipher HI:
pHaplo:
pTriplo:
SPDYE8 (whole gene)
Position: chr7-73019719-73029766
Region Type: GENE
Protein Coding: Yes
LoF pLI:
Decipher HI:
pHaplo:
pTriplo:
SPDYE9 (whole gene)
Position: chr7-73075972-73086038
Region Type: GENE
Protein Coding: Yes
LoF pLI:
Decipher HI:
pHaplo:
pTriplo:
STX1A (whole gene)
Position: chr7-73699210-73719669
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.0
Decipher HI: 0.23
pHaplo:
pTriplo:
TBL2 (whole gene)
Position: chr7-73567537-73578579
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.4e-9
Decipher HI: 0.31
pHaplo:
pTriplo:
TMEM270 (whole gene)
Position: chr7-73861159-73865890
Region Type: GENE
Protein Coding: Yes
LoF pLI: 4.1e-11
Decipher HI:
pHaplo:
pTriplo:
TRIM50 (whole gene)
Position: chr7-73312536-73328082
Region Type: GENE
Protein Coding: Yes
LoF pLI: 4.9e-10
Decipher HI: 0.56
pHaplo:
pTriplo:
TRIM74 (whole gene)
Position: chr7-72959485-72969466
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.23
Decipher HI: 0.83
pHaplo:
pTriplo:
VPS37D (whole gene)
Position: chr7-73667831-73672110
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.26
Decipher HI: 0.64
pHaplo:
pTriplo:
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Debug
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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_148912.4",
"chr": "7",
"start": 73736094,
"end": 73738802,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 16407,
"geneSummaryLongCarrier": {
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"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": {
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"cdsFractionLost": 1,
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"exonsBasesSize": 1418,
"exonsFractionLost": 1,
"lostExons": 6,
"lostExonsRanks": [
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],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_032408.4",
"chr": "7",
"start": 73440406,
"end": 73522293,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 961,
"geneSummaryLongCarrier": {
"inheritances": [
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],
"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,
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"exonsFractionLost": 1,
"lostExons": 20,
"lostExonsRanks": [
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"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_001707.4",
"chr": "7",
"start": 73536356,
"end": 73557690,
"regionType": "GENE",
"overlapType": "FULL",
"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": {
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"readingFrameDestroyed": false,
"overlapType": "FULL",
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"escapeNmd": false
}
},
{
"id": "NM_017528.5",
"chr": "7",
"start": 73683597,
"end": 73698212,
"regionType": "GENE",
"overlapType": "FULL",
"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": {
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"cdsFractionLost": 1,
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"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_001306.4",
"chr": "7",
"start": 73768997,
"end": 73770270,
"regionType": "GENE",
"overlapType": "FULL",
"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": {
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"exonsBasesSize": 1274,
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"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_001305.5",
"chr": "7",
"start": 73830996,
"end": 73832690,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 2046,
"geneSummaryLongCarrier": {
"symbol": "CLDN4",
"proteinCoding": true,
"maneSelectEnsemblId": "ENST00000340958.4",
"maneSelectRefSeqId": "NM_001305.5",
"lof_pLI": 0.00012713,
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"overlapType": "FULL",
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}
},
{
"id": "NM_032317.3",
"chr": "7",
"start": 73680918,
"end": 73683453,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 16410,
"geneSummaryLongCarrier": {
"inheritances": [
"Mitochondrial",
"AR"
],
"diseaseAssociations": [
{
"classification": "SUPPORTIVE",
"diseaseName": "Leber hereditary optic neuropathy",
"diseaseId": "MONDO:0010788",
"inheritanceMode": "Mitochondrial",
"source": "GENCC"
},
{
"classification": "STRONG",
"diseaseName": "Leber hereditary optic neuropathy, autosomal recessive",
"diseaseId": "MONDO:0030309",
"inheritanceMode": null,
"source": "GENCC"
},
{
"classification": "LIMITED",
"diseaseName": "Leber hereditary optic neuropathy, autosomal recessive",
"diseaseId": "MONDO:0030309",
"inheritanceMode": null,
"source": "GENCC"
}
],
"symbol": "DNAJC30",
"proteinCoding": true,
"maneSelectEnsemblId": "ENST00000395176.3",
"maneSelectRefSeqId": "NM_032317.3",
"lof_pLI": 5.8209e-7,
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"decipherHi": 0.8016,
"geneGroup": "DNAJ (HSP40) heat shock proteins"
},
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"readingFrameDestroyed": false,
"overlapType": "FULL",
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"escapeNmd": false
}
},
{
"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,
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"decipherHi": 0.2178,
"geneGroup": "RNA binding motif containing|MicroRNA protein coding host genes"
},
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"overlapType": "FIVE_UTR_WITH_CDS",
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}
},
{
"id": "NM_000501.4",
"chr": "7",
"start": 74028173,
"end": 74069907,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 3327,
"geneSummaryLongCarrier": {
"inheritances": [
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],
"diseaseAssociations": [
{
"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": "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"
},
{
"classification": "LIMITED",
"diseaseName": "familial thoracic aortic aneurysm and aortic dissection",
"diseaseId": "MONDO:0019625",
"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,
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"lostExonsRanks": [
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32
],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 142,
"escapeNmd": false
},
"phenotypeHi": "MONDO:0008504",
"triploinsufficiencyType": "NO_EVIDENCE_AVAILABLE",
"haploinsufficiencyType": "SUFFICIENT_EVIDENCE"
},
{
"id": "NM_003602.5",
"chr": "7",
"start": 73328161,
"end": 73358625,
"regionType": "GENE",
"overlapType": "FULL",
"coveredFraction": 1,
"hgncId": 3722,
"geneSummaryLongCarrier": {
"inheritances": [
"AR"
],
"diseaseAssociations": [
{
"classification": "MODERATE",
"diseaseName": "spermatogenic failure 77",
"diseaseId": "MONDO:0031083",
"inheritanceMode": null,
"source": "GENCC"
}
],
"symbol": "FKBP6",
"proteinCoding": true,
"maneSelectEnsemblId": "ENST00000252037.5",
"maneSelectRefSeqId": "NM_003602.5",
"lof_pLI": 0.0000039823,
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"acmg": {
"position": {
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},
"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:nssv15129678. "
},
{
"criterium": "LOSS_2A",
"report": "There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv17955650, dbVar:nssv18791887, dbVar:nssv15128578, dbVar:nssv17971140, dbVar:nssv15130169, dbVar:nssv16214480, dbVar:nssv15770120, dbVar:nssv17172746, dbVar:nssv15137072, dbVar:nssv15128343, dbVar:nssv18786274, HI3:ELN, dbVar:nssv15140244, morbid:FKBP6, dbVar:nssv15147201, dbVar:nssv16208140, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15167740. Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650, dbVar:nssv15137072, dbVar:nssv15128343, HI3:ELN, morbid:FKBP6, dbVar:nssv16208140, morbid:DNAJC30. "
},
{
"criterium": "LOSS_2A",
"report": "There is complete overlap with established HI gene(s): ELN. There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv17955650, dbVar:nssv18791887, dbVar:nssv15128578, dbVar:nssv17971140, dbVar:nssv15130169, dbVar:nssv16214480, dbVar:nssv15770120, dbVar:nssv17172746, dbVar:nssv15137072, dbVar:nssv15128343, dbVar:nssv18786274, HI3:ELN, dbVar:nssv15140244, morbid:FKBP6, dbVar:nssv15147201, dbVar:nssv16208140, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15167740. Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650, dbVar:nssv15137072, dbVar:nssv15128343, HI3:ELN, morbid:FKBP6, dbVar:nssv16208140, morbid:DNAJC30. "
},
{
"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:nssv15129678. ",
"met": true,
"points": 0
},
{
"criterium": "LOSS_2A",
"report": "There is complete overlap with established HI gene(s): ELN. There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN, dbVar:nssv16214500, dbVar:nssv15130113, dbVar:nssv17955650, dbVar:nssv18791887, dbVar:nssv15128578, dbVar:nssv17971140, dbVar:nssv15130169, dbVar:nssv16214480, dbVar:nssv15770120, dbVar:nssv17172746, dbVar:nssv15137072, dbVar:nssv15128343, dbVar:nssv18786274, HI3:ELN, dbVar:nssv15140244, morbid:FKBP6, dbVar:nssv15147201, dbVar:nssv16208140, morbid:DNAJC30, dbVar:nssv18791884, dbVar:nssv15167740. Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650, dbVar:nssv15137072, dbVar:nssv15128343, HI3:ELN, morbid:FKBP6, dbVar:nssv16208140, morbid:DNAJC30. ",
"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 over established HI gene(s): ELN. There is complete overlap with established HI region(s): dbVar:nssv16213814, morbid:ELN (and 21 more). Among those, regions with breakpoints not laying inside the transcripts: morbid:ELN, dbVar:nssv17955650 (and 6 more). ClinGen associates these changes with phenotype(s): MONDO:0008504. 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
},
"liftedFrom": null,
"userQuery": "7:72846244-74187855 DEL"
}