View genomic variant #0000000160
Chromosome |
1 |
Allele |
Unknown |
Affects function (as reported) |
Affects function |
Affects function (by curator) |
Affects function |
Type |
del |
DNA change (genomic) (Relative to hg19 / GRCh37) |
g.216420437del |
Published as |
- |
GERP |
2.370 |
Segregation |
- |
DB-ID |
USH2A_000018 |
MSCV |
MSCV_0000160 |
dbSNP ID |
rs80338903 |
Frequency |
- |
Sources |
; clinVar; Ensembl; |
Reference |
12112664;14970843;20301515;10909849;11402400;10729113;15025721 |
Variant remarks |
- |
Genetic origin |
- |
Variant_disease |
- |
Average frequency (large NGS studies) |
0.00096 View details |
Owner |
LOVD |
Variant on transcripts
ClinVar @ MSeqDR | RCVaccession | RCV000002445; RCV000032524; RCV000191141; RCV000210326; RCV000254870; RCV000504641; RCV000623326; RCV000735362; RCV000787897; RCV000787899; RCV000824793; RCV000787895; RCV001000453; RCV001095692; RCV002504737; RCV003398418; | Chromosome | 1:216420437..216420437 | Allele frequencies from ESP | 0.00096 | Allele frequencies from ExAC | 0.00079 | ClinVar Allele ID | 17390 | Disease database name and identifier | Human Phenotype Ontology:HP:0040070, MedGen:C4022458|Human Phenotype Ontology:HP:0005684, MONDO:MONDO:0019942, MedGen:C0265213, OMIM:PS108120, Orphanet:97120|Human Phenotype Ontology:HP:0002128, Human Phenotype Ontology:HP:0002129, Human Phenotype Ontology:HP:0002302, Human Phenotype Ontology:HP:0002337, Human Phenotype Ontology:HP:0002441, Human Phenotype Ontology:HP:0006972, Human Phenotype Ontology:HP:0006998, Human Phenotype Ontology:HP:0007211, Human Phenotype Ontology:HP:0100543, MedGen:C0338656|Human Phenotype Ontology:HP:0002975, Human Phenotype Ontology:HP:0003083, Human Phenotype Ontology:HP:0005673, Human Phenotype Ontology:HP:0005836, MedGen:C0265563|Human Phenotype Ontology:HP:0001348, MedGen:C2673700|Human Phenotype Ontology:HP:0000739, MONDO:MONDO:0011918, MedGen:C0003467, OMIM:607834|Human Phenotype Ontology:HP:0000156, Human Phenotype Ontology:HP:0000218, Human Phenotype Ontology:HP:0009080, Human Phenotype Ontology:HP:0009082, Human Phenotype Ontology:HP:0009097, MedGen:C0240635|Human Phenotype Ontology:HP:0012532, MedGen:C0150055|Human Phenotype Ontology:HP:0002817, Human Phenotype Ontology:HP:0003838, MedGen:C4020900|Human Phenotype Ontology:HP:0002828, MedGen:C0158118|Human Phenotype Ontology:HP:0001509, Human Phenotype Ontology:HP:0003501, Human Phenotype Ontology:HP:0003507, Human Phenotype Ontology:HP:0003512, Human Phenotype Ontology:HP:0003518, Human Phenotype Ontology:HP:0003519, Human Phenotype Ontology:HP:0004322, Human Phenotype Ontology:HP:0008871, Human Phenotype Ontology:HP:0008882, Human Phenotype Ontology:HP:0008888, Human Phenotype Ontology:HP:0008913, MedGen:C0349588|Human Phenotype Ontology:HP:0002387, Human Phenotype Ontology:HP:0002459, Human Phenotype Ontology:HP:0007310, Human Phenotype Ontology:HP:0012332, MONDO:MONDO:0044872, MedGen:C0013363|Human Phenotype Ontology:HP:0009810, MedGen:C4021387|MONDO:MONDO:0019501, MeSH:D052245, MedGen:C0271097, OMIM:PS276900, Orphanet:886|MeSH:D030342, MedGen:C0950123|.|MedGen:C5680250, Orphanet:96210|Human Phenotype Ontology:HP:0007638, Human Phenotype Ontology:HP:0007754, Human Phenotype Ontology:HP:0007798, Human Phenotype Ontology:HP:0007914, Human Phenotype Ontology:HP:0007919, Human Phenotype Ontology:HP:0007999, MedGen:C0730292|MedGen:CN239332|Human Phenotype Ontology:HP:0007642, Human Phenotype Ontology:HP:0007684, Human Phenotype Ontology:HP:0007861, Human Phenotype Ontology:HP:0007953, MONDO:MONDO:0016293, MedGen:C0339535, OMIM:PS310500, Orphanet:215|Human Phenotype Ontology:HP:0000556, Human Phenotype Ontology:HP:0007736, Human Phenotype Ontology:HP:0007910, Human Phenotype Ontology:HP:0007974, Human Phenotype Ontology:HP:0007982, MONDO:MONDO:0019118, MeSH:D058499, MedGen:C0854723, Orphanet:71862|MONDO:MONDO:0010169, MedGen:C1848634, OMIM:276901, Orphanet:231178, Orphanet:886|MONDO:MONDO:0013436, MedGen:C3151138, OMIM:613809, Orphanet:791|MedGen:C3661900|MedGen:CN169374|Human Phenotype Ontology:HP:0000547, MONDO:MONDO:0019200, MeSH:D012174, MedGen:C0035334, OMIM:268000, OMIM:PS268000, Orphanet:791|Human Phenotype Ontology:HP:0000548, MONDO:MONDO:0015993, MedGen:C4085590, OMIM:PS120970, Orphanet:1872 | ClinVar preferred disease name | Abnormal upper limb bone morphology|Distal arthrogryposis|Cognitive impairment|Dislocated radial head|Brisk reflexes|Anxiety|High palate|Chronic pain|Abnormality of the upper limb|Multiple joint contractures|Short stature|Abnormal autonomic nervous system physiology|Abnormality of upper limb joint|Usher syndrome|Inborn genetic diseases|USH2A-related condition|Rare genetic deafness|Macular dystrophy|USH2A-Related Disorders|Congenital stationary night blindness|Retinal dystrophy|Usher syndrome type 2A|Retinitis pigmentosa 39|not provided|not specified|Retinitis pigmentosa|Cone/cone-rod dystrophy | HGVS variant names | NC 000001.10:g.216420437del | ClinVar review status | criteria provided, conflicting interpretations | Clinical Significance | Conflicting interpretations of pathogenicity | Conflicting clinical significance | Pathogenic(33)|Uncertain significance(1) | Variant type | Deletion | Sequence Ontology for variant type | SO:0000159 | Variant clinical sources reported | ClinGen:CA252226|OMIM:608400.0001 | Gene symbol:Gene id. | USH2A:7399 | Molecular consequence | SO:0001589|frameshift variant | Allele origin | | dbSNP ID | 80338903 | For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN | MONDO:MONDO:0010169, MedGen:C1848634, OMIM:276901, Orphanet:231178, Orphanet:886 | For included Variant : ClinVar preferred disease name for the concept specified by disease identifiers in CLNDISDB | Usher syndrome type 2A | Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance. | 560516:Pathogenic | Variant Flags | : |
ClinVar @ MSeqDR as full content XML tree
MSeqDR View Variant at Gbrowse Mitomap Mitochondrial Variant Phenotype Information:
None Ensembl Variant Phenotype Information:
None
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