Length (hg38) : 594,340 bases - Length (hg19) : 206,231 bases
CNV-Hub AChro-Puce
Benign
AChro-Puce Criteria taken into account 1
1
2 Major
2 Minor
ISV 2
XCNV 3
ClassifyCNV ACMG 4
AnnotSV ACMG 5
ACMG criteria
ClassifyCNV
AnnotSV
ClinGen
0 benign CNV0 likely benign CNV
0 uncertain CNV
0 likely pathogenic CNV
0 pathogenic CNV
70% Overlaps
Decipher
1 benign CNV1 unknown CNV
0 uncertain CNV
0 pathogenic CNV
70% Overlaps
DGV-Gold
0
80% Overlaps
0
50% Overlaps
DGV
10
80% Overlaps
30
50% Overlaps
Coe & Al study 6
0
Patient cases
70% Overlaps
0
Controls
70% Overlaps
Genes with pTriplo > 0.68 7
0
Genes with pHaplo > 0.55 7
0
Genes in SFARI
0
Genes in OMIM
5
Sources and references
1 : AChroPuce Consortium Recommandations pour l’interpretation Clinique des CNV (Copy Number Variations) Septembre 2022.
2 : Automated prediction of the clinical impact of structural copy number variations : M. Gažiová, T. Sládeček, O. Pös, M. Števko, W. Krampl, Z. Pös, R. Hekel, M. Hlavačka, M. Kucharík, J. Radvánszky, J. Budiš & T. Szemes View article
3 : Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, et al X CNV genome wide prediction of the pathogenicity of copy number variations Genome Med 2021 13 132.
4 : Gurbich, T.A., Ilinsky, V.V. ClassifyCNV: a tool for clinical annotation of copy-number variants. Sci Rep 10, 20375 (2020). View article
5 : Geoffroy V, Herenger Y, Kress A, et al. AnnotSV: an integrated tool for structural variations annotation. Bioinforma Oxf Engl. 2018;34(20):3572-3574. doi:10.1093/bioinformatics/bty304
6 : Coe BP, Witherspoon K, Rosenfeld JA, van Bon BWM, Vulto van Silfhout AT, Bosco P, et al Refining analyses of copy number variation identifies specific genes associated with developmental delay Nat Genet 2014 46 1063 71
7 : Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, et al A cross disorder dosage sensitivity map of the human genome Cell 2022 185 3041 3055 e 25
0 Microdeletion and microduplication syndromes from litterature (>= 70% only)
5 OMIM Gene overlap(s)
Download genes as .csv
Location : 46,911,396 - 47,002,488
Database :
DecipherGenomics OMIM:610630 GTEx Portal Human Protein Atlas Ensembl
Location : 47,460,162 - 47,484,158
Database :
DecipherGenomics OMIM:602396 GTEx Portal Human Protein Atlas Ensembl
Location : 47,300,197 - 47,313,577
Database :
DecipherGenomics OMIM:601361 GTEx Portal Human Protein Atlas Ensembl
Location : 47,348,363 - 47,357,881
Database :
DecipherGenomics PanelApp OMIM:180290 GTEx Portal Human Protein Atlas Ensembl
Human Phenotype Ontology Show/Hide
| HP:0000501 | Glaucoma | Glaucoma refers loss of retinal ganglion cells in a characteristic pattern of optic neuropathy usually associated with increased intraocular pressure. |
|---|---|---|
| HP:0000510 | Rod-cone dystrophy | An inherited retinal disease subtype in which the rod photoreceptors appear to be more severely affected than the cone photoreceptors. Typical presentation is with nyctalopia (due to rod dysfunction) followed by loss of mid-peripheral field of vision, which gradually extends and leaves many patients with a small central island of vision due to the preservation of macular cones. |
| HP:0001419 | X-linked recessive inheritance | A mode of inheritance that is observed for recessive traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked recessive disorders manifest in males (who have one copy of the X chromosome and are thus hemizygotes), but generally not in female heterozygotes who have one mutant and one normal allele. |
| HP:0007663 | Reduced visual acuity | |
| HP:0005978 | Type II diabetes mellitus | A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. |
| HP:0000842 | Hyperinsulinemia | An increased concentration of insulin in the blood. |
| HP:0008046 | Abnormal retinal vascular morphology | A structural abnormality of retinal vasculature. |
| HP:0003581 | Adult onset | Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. |
| HP:0000543 | Optic disc pallor | A pale yellow discoloration of the optic disk (the area of the optic nerve head in the retina). The optic disc normally has a pinkish hue with a central yellowish depression. |
| HP:0000007 | Autosomal recessive inheritance | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele). |
| HP:0000431 | Wide nasal bridge | Increased breadth of the nasal bridge (and with it, the nasal root). |
| HP:0007675 | Progressive night blindness | |
| HP:0001133 | Constriction of peripheral visual field | An absolute or relative decrease in retinal sensitivity extending from edge (periphery) of the visual field in a concentric pattern. The visual field is the area that is perceived simultaneously by a fixating eye. |
| HP:0031605 | Abnormality of fundus pigmentation | Any anomaly of the pigmentation of the fundus, the posterior part of the eye including the retina and optic nerve. |
| HP:0000987 | Atypical scarring of skin | Atypically scarred skin . |
| HP:0000613 | Photophobia | Excessive sensitivity to light with the sensation of discomfort or pain in the eyes due to exposure to bright light. |
| HP:0000648 | Optic atrophy | Atrophy of the optic nerve. Optic atrophy results from the death of the retinal ganglion cell axons that comprise the optic nerve and manifesting as a pale optic nerve on fundoscopy. |
| HP:0007703 | Abnormality of retinal pigmentation | |
| HP:0000563 | Keratoconus | A cone-shaped deformity of the cornea characterized by the presence of corneal distortion secondary to thinning of the apex. |
| HP:0000463 | Anteverted nares | Anteriorly-facing nostrils viewed with the head in the Frankfurt horizontal and the eyes of the observer level with the eyes of the subject. This gives the appearance of an upturned nose (upturned nasal tip). |
| HP:0000505 | Visual impairment | Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. |
| HP:0000006 | Autosomal dominant inheritance | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele. |
| HP:0000639 | Nystagmus | Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms. |
| HP:0000518 | Cataract | A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule. |
| HP:0000602 | Ophthalmoplegia | Paralysis of one or more extraocular muscles that are responsible for eye movements. |
| HP:0001249 | Intellectual disability | Intellectual disability, previously referred to as mental retardation, is characterized by subnormal intellectual functioning that occurs during the developmental period. It is defined by an IQ score below 70. |
| HP:0000405 | Conductive hearing impairment | An abnormality of vibrational conductance of sound to the inner ear leading to impairment of sensory perception of sound. |
| HP:0000662 | Nyctalopia | Inability to see well at night or in poor light. |
| HP:0007737 | Bone spicule pigmentation of the retina | Pigment migration into the retina in a bone-spicule configuration (resembling the nucleated cells within the lacuna of bone). |
| HP:0000035 | Abnormal testis morphology | An anomaly of the testicle (the male gonad). |
| HP:0000603 | Central scotoma | An area of depressed vision located at the point of fixation and that interferes with central vision. |
| HP:0000618 | Blindness | Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degrees in radius around central fixation. |
| HP:0008736 | Hypoplasia of penis | |
| HP:0001513 | Obesity | Accumulation of substantial excess body fat. |
| HP:0000135 | Hypogonadism | A decreased functionality of the gonad. |
| HP:0000407 | Sensorineural hearing impairment | A type of hearing impairment in one or both ears related to an abnormal functionality of the cochlear nerve. |
| HP:0001347 | Hyperreflexia | Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles. |
| HP:0000512 | Abnormal electroretinogram | Any abnormality of the electrical responses of various cell types in the retina as measured by electroretinography. |
| HP:0007787 | Posterior subcapsular cataract | A type of cataract affecting the posterior pole of lens immediately adjacent to ('beneath') the Lens capsule. |
Location : 47,322,454 - 47,327,588
Database :
DecipherGenomics PanelApp OMIM:605120 GTEx Portal Human Protein Atlas Ensembl
Human Phenotype Ontology Show/Hide
| HP:0002092 | Pulmonary arterial hypertension | Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position. |
|---|---|---|
| HP:0100659 | Abnormal cerebral vascular morphology | An anomaly of the cerebral blood vessels. |
| HP:0001409 | Portal hypertension | Increased pressure in the portal vein. |
| HP:0002040 | Esophageal varix | Extreme dilation of the submucusoal veins in the lower portion of the esophagus. |
| HP:0011025 | Abnormal cardiovascular system physiology | Abnormal functionality of the cardiovascular system. |
| HP:0001250 | Seizure | A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. |
| HP:0000787 | Nephrolithiasis | The presence of calculi (stones) in the kidneys. |
| HP:0000421 | Epistaxis | Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. |
| HP:0007420 | Spontaneous hematomas | Spontaneous development of hematomas (hematoma) or bruises without significant trauma. |
| HP:0002910 | Elevated hepatic transaminase | Elevations of the levels of SGOT and SGPT in the serum. SGOT (serum glutamic oxaloacetic transaminase) and SGPT (serum glutamic pyruvic transaminase) are transaminases primarily found in the liver and heart and are released into the bloodstream as the result of liver or heart damage. SGOT and SGPT are used clinically mainly as markers of liver damage. |
| HP:0001082 | Cholecystitis | The presence of inflammatory changes in the gallbladder. |
| HP:0001342 | Cerebral hemorrhage | Hemorrhage into the parenchyma of the brain. |
| HP:0001009 | Telangiectasia | Telangiectasias refer to small dilated blood vessels located near the surface of the skin or mucous membranes, measuring between 0.5 and 1 millimeter in diameter. Telangiectasia are located especially on the tongue, lips, palate, fingers, face, conjunctiva, trunk, nail beds, and fingertips. |
| HP:0000524 | Conjunctival telangiectasia | The presence of small (ca. 0.5-1.0 mm) dilated blood vessels near the surface of the mucous membranes of the conjunctiva. |
| HP:0002138 | Subarachnoid hemorrhage | Hemorrhage occurring between the arachnoid mater and the pia mater. |
| HP:0100585 | Telangiectasia of the skin | Presence of small, permanently dilated blood vessels near the surface of the skin, visible as small focal red lesions. |
| HP:0100761 | Visceral angiomatosis | |
| HP:0001394 | Cirrhosis | A chronic disorder of the liver in which liver tissue becomes scarred and is partially replaced by regenerative nodules and fibrotic tissue resulting in loss of liver function. |
| HP:0001635 | Congestive heart failure | The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. |
| HP:0002105 | Hemoptysis | Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs. |
| HP:0000646 | Amblyopia | Reduced visual acuity that is uncorrectable by lenses in the absence of detectable anatomic defects in the eye or visual pathways. |
| HP:0000790 | Hematuria | The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). |
| HP:0001048 | Cavernous hemangioma | The presence of a cavernous hemangioma. A hemangioma characterized by large endothelial spaces (caverns) is called a cavernous hemangioma. |
| HP:0100784 | Peripheral arteriovenous fistula | |
| HP:0002204 | Pulmonary embolism | An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. |
| HP:0000006 | Autosomal dominant inheritance | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele. |
| HP:0001399 | Hepatic failure | |
| HP:0004936 | Venous thrombosis | Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. |
| HP:0100026 | Arteriovenous malformation | An anomalous configuration of blood vessels that shunts arterial blood directly into veins without passing through the capillaries. |
| HP:0001935 | Microcytic anemia | A kind of anemia in which the volume of the red blood cells is reduced. |
| HP:0002326 | Transient ischemic attack | |
| HP:0200008 | Intestinal polyposis | The presence of multiple polyps in the intestine. |
| HP:0004406 | Spontaneous, recurrent epistaxis | |
| HP:0002239 | Gastrointestinal hemorrhage | Hemorrhage affecting the gastrointestinal tract. |
| HP:0002076 | Migraine | Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. |
| HP:0001081 | Cholelithiasis | Hard, pebble-like deposits that form within the gallbladder. |
| HP:0007763 | Retinal telangiectasia | Dilatation of small blood vessels of the retina. |
| HP:0100579 | Mucosal telangiectasiae | Telangiectasia of the mucosa, the mucous membranes which are involved in absorption and secretion that line cavities that are exposed to the external environment and internal organs. |
12 Non-OMIM Gene overlap(s)
ENSG00000254929
Size : 35,698 bases
Location : 47,517,816 - 47,553,514
AGAP9
Size : 21,784 bases
Location : 47,501,854 - 47,523,638
ENSG00000289299
Size : 17,549 bases
Location : 47,207,445 - 47,224,994
ZNF488
Size : 18,797 bases
Location : 47,365,496 - 47,384,293
ENSG00000290453
Size : 13,577 bases
Location : 47,538,377 - 47,551,954
BMS1P2
Size : 11,842 bases
Location : 47,540,077 - 47,551,919
ENSG00000224919
Size : 5,983 bases
Location : 47,496,212 - 47,502,195
ENSG00000265630
Size : 6,093 bases
Location : 47,563,604 - 47,569,697
FAM25G
Size : 4,481 bases
Location : 47,487,219 - 47,491,700
DUSP8P1
Size : 1,760 bases
Location : 47,564,256 - 47,566,016
RNA5SP312
Size : 115 bases
Location : 47,532,352 - 47,532,467
ENSG00000270369
Size : 297 bases
Location : 47,484,457 - 47,484,754
0 ClinGen CNV overlap(s) (>= 70% only)
0 Benign CNV 0 Likely benign CNV 0 Uncertain CNV 0 Likely pathogenic CNV 0 Pathogenic CNV
2 Decipher CNV overlap(s) (>= 70% only)
1 Benign CNV 1 Unknown CNV 0 Uncertain CNV 0 Pathogenic CNV
#1 : unknown
Location : 47,011,583 - 47,655,146
| Size : 643,563 bases
Patient Id : 300081
Gender : Inconnu
Phenotype :
Abnormal facial shape, Anorexia, Scoliosis, Abnormal facial shape, Anorexia, Scoliosis
#2 : benign
Location : 46,699,488 - 47,655,117
| Size : 955,629 bases
Patient Id : 297070
Gender : Inconnu
Phenotype :
Cleft palate, Cleft palate, Cleft palate, Cleft palate
0 Gene(s) in SFARI Database
0 DGV-Gold overlap(s) (>= 50% only)
30 DGV overlap(s) (>= 50% only)
DGV #1
Location : 46,977,295 - 47,632,739
| Size : 655,444 bases
DGV #2
Location : 46,674,168 - 47,967,299
| Size : 1,293,131 bases
DGV #3
Location : 46,527,665 - 47,392,320
| Size : 864,655 bases
DGV #4
Location : 46,990,727 - 47,703,613
| Size : 712,886 bases
DGV #5
Location : 46,527,665 - 47,743,504
| Size : 1,215,839 bases
DGV #6
Location : 46,961,233 - 47,546,323
| Size : 585,090 bases
DGV #7
Location : 46,990,728 - 47,703,613
| Size : 712,885 bases
DGV #8
Location : 47,003,692 - 47,743,504
| Size : 739,812 bases
DGV #9
Location : 46,590,219 - 47,392,320
| Size : 802,101 bases
DGV #10
Location : 46,918,172 - 48,036,559
| Size : 1,118,387 bases
DGV #11
Location : 46,216,415 - 47,742,094
| Size : 1,525,679 bases
DGV #12
Location : 46,918,172 - 47,249,575
| Size : 331,403 bases
DGV #13
Location : 47,076,674 - 48,006,310
| Size : 929,636 bases
DGV #14
Location : 46,954,483 - 47,249,575
| Size : 295,092 bases
DGV #15
Location : 47,025,092 - 47,392,320
| Size : 367,228 bases
DGV #16
Location : 46,996,905 - 47,392,332
| Size : 395,427 bases
DGV #17
Location : 46,287,822 - 47,692,945
| Size : 1,405,123 bases
DGV #18
Location : 46,943,377 - 47,704,625
| Size : 761,248 bases
DGV #19
Location : 46,674,168 - 47,703,613
| Size : 1,029,445 bases
DGV #20
Location : 46,949,255 - 47,185,089
| Size : 235,834 bases
DGV #21
Location : 47,028,331 - 47,741,882
| Size : 713,551 bases
DGV #22
Location : 47,046,997 - 47,392,320
| Size : 345,323 bases
DGV #23
Location : 46,918,172 - 47,392,320
| Size : 474,148 bases
DGV #24
Location : 46,247,355 - 47,743,504
| Size : 1,496,149 bases
DGV #25
Location : 46,918,172 - 47,743,504
| Size : 825,332 bases
DGV #26
Location : 46,478,317 - 47,429,141
| Size : 950,824 bases
DGV #27
Location : 46,966,534 - 47,692,945
| Size : 726,411 bases
DGV #28
Location : 47,112,087 - 47,743,504
| Size : 631,417 bases
DGV #29
Location : 46,943,377 - 47,742,094
| Size : 798,717 bases
DGV #30
Location : 46,966,534 - 48,298,893
| Size : 1,332,359 bases
0 Patient cases (>= 70% only)
0 Controls (>= 70% only)
2 Gene(s) in PanelApp Database
| Confidence | Disease | Inheritance | Phenotype | Evidence |
|---|---|---|---|---|
| Low | Glaucoma (developmental) |
- Eye Disorders |
- NHS GMS - Emory Genetics Laboratory |
|
| High | Retinal disorders | BIALLELIC, autosomal or pseudoautosomal |
- Eye Disorders - Retinitis Pigmentosa, Recessive - Retinitis pigmentosa - ?Retinitis pigmentosa 66, 615233 |
- NHS GMS - Expert Review Green |
| Low | Structural eye disease | BIALLELIC, autosomal or pseudoautosomal |
- ?Retinitis pigmentosa 66, 615233 - Eye Disorders |
- NHS GMS - Expert Review Red |
| Confidence | Disease | Inheritance | Phenotype | Evidence |
|---|---|---|---|---|
| Medium | Cerebral vascular malformations | MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
- Telangiectasia, hereditary hemorrhagic, type 5, OMIM:615506 |
- Yorkshire and North East GLH - NHS GMS - Expert Review Amber - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory |
| High | Hereditary haemorrhagic telangiectasia | MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
- Telangiectasia, hereditary hemorrhagic, type 5 OMIM:615506 - telangiectasia, hereditary hemorrhagic, type 5 MONDO:0014217 |
- Expert Review Green - NHS GMS - Expert Review - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory |
| High | Pulmonary arterial hypertension | MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
- Heritable pulmonary arterial hypertension - HPAH |
- NHS GMS - Expert Review Green - Literature |
| Low | Fetal anomalies | BIALLELIC, autosomal or pseudoautosomal |
- Lymphatic dysplasia - hydrothorax - hydrops |
- Expert Review Red - Literature |