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 over established HI gene(s): LIMK1, ELN. 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). 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
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 gene(s): LIMK1, ELN. 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
Genes affected
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:
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:
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:
TMEM270 (whole gene)
Position: chr7-73861159-73865890
Region Type: GENE
Protein Coding: Yes
LoF pLI: 4.1e-11
Decipher HI:
pHaplo:
pTriplo:
METTL27 (whole gene)
Position: chr7-73834590-73842516
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.8e-12
Decipher HI:
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:
CLDN3 (whole gene)
Position: chr7-73768997-73770270
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.45
Decipher HI: 0.33
pHaplo:
pTriplo:
ABHD11 (whole gene)
Position: chr7-73736094-73738802
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.9e-8
Decipher HI: 0.77
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:
BUD23 (whole gene)
Position: chr7-73683597-73698212
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.9e-8
Decipher HI:
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:
VPS37D (whole gene)
Position: chr7-73667831-73672110
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.26
Decipher HI: 0.64
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:
TBL2 (whole gene)
Position: chr7-73567537-73578579
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.4e-9
Decipher HI: 0.31
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:
BAZ1B (whole gene)
Position: chr7-73440406-73522293
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.0
Decipher HI: 0.24
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:
FKBP6 (whole gene)
Position: chr7-73328161-73358625
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.0000040
Decipher HI: 0.66
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:
NSUN5 (whole gene)
Position: chr7-73302516-73308826
Region Type: GENE
Protein Coding: Yes
LoF pLI: 1.1e-10
Decipher HI: 0.70
pHaplo:
pTriplo:
SPDYE10 (whole gene)
Position: chr7-73104008-73155431
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:
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:
TRIM74 (whole gene)
Position: chr7-72959485-72969466
Region Type: GENE
Protein Coding: Yes
LoF pLI: 0.23
Decipher HI: 0.83
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:
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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",
"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,
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],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"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",
"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": [
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3,
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23,
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25,
26,
27,
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29,
30,
31,
32
],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 124,
"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",
"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",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_152559.3",
"chr": "7",
"start": 73834590,
"end": 73842516,
"regionType": "GENE",
"overlapType": "FULL",
"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": [
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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,
"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": [
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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": {
"cdsBasesLost": 663,
"cdsBasesSize": 663,
"cdsFractionLost": 1,
"exonsBasesLost": 1274,
"exonsBasesSize": 1274,
"exonsFractionLost": 1,
"lostExons": 1,
"lostExonsRanks": [
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],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_148912.4",
"chr": "7",
"start": 73736094,
"end": 73738802,
"regionType": "GENE",
"overlapType": "FULL",
"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": [
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3,
4,
5
],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"id": "NM_004603.4",
"chr": "7",
"start": 73699210,
"end": 73719669,
"regionType": "GENE",
"overlapType": "FULL",
"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,
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5,
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7,
8,
9
],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 6,
"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": {
"cdsBasesLost": 846,
"cdsBasesSize": 846,
"cdsFractionLost": 1,
"exonsBasesLost": 1201,
"exonsBasesSize": 1201,
"exonsFractionLost": 1,
"lostExons": 12,
"lostExonsRanks": [
0,
1,
2,
3,
4,
5,
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7,
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11
],
"readingFrameDestroyed": false,
"overlapType": "FULL",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
"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"
},
{
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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: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_2A",
"report": "There is complete overlap with established HI gene(s): LIMK1, ELN. 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 gene(s): LIMK1, ELN. 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 over established HI gene(s): LIMK1, ELN. 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). 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
}
}