View genomic variant #0000015669

Variant on transcripts

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Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.

Protein: Description of variant at protein level (following HGVS recommendations).

• p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
• p.Arg345Pro = change derived from RNA analysis
• p.? = unknown effect
• p.0? = probably no protein produced

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

• intergenic
• near-gene-5
• utr-5
• coding
• coding-near-splice
• coding-synonymous
• coding-synonymous-near-splice
• codingComplex
• codingComplex-near-splice
• frameshift
• frameshift-near-splice
• missense
• missense-near-splice
• splice-5
• intron
• splice-3
• stop-gained
• stop-gained-near-splice
• stop-lost
• stop-lost-near-splice
• utr-3
• near-gene-3

Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

• benign = Benign
• possiblyDamaging = Possibly damaging
• probablyDamaging = Probably damaging
• noPrediction = No prediction

RNA change: Description of variant at RNA level (following HGVS recommendations).

• r.123c>u
• r.? = unknown
• r.(?) = RNA not analysed but probably transcribed copy of DNA variant
• r.spl? = RNA not analysed but variant probably affects splicing
• r.(spl?) = RNA not analysed but variant may affect splicing
• r.0? = change expected to abolish transcription

SIFT: SIFT Annotation

2 entries on 1 page. Showing entries 1 - 2.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
USH2A	00003116	NM_007123.5	0000015669	./.	c.4252-13_4252-12insCTTT	p.(=)	-	-	-	-	r.(=)	-
USH2A	00003348	NM_206933.2	0000015669	./.	c.4252-13_4252-12insCTTT	p.(=)	-	-	-	-	r.(=)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV003084327;
Chromosome	1:216363721..216363722
ClinVar Allele ID	1905770
Disease database name and identifier	MedGen:CN517202
ClinVar preferred disease name	not provided
HGVS variant names	NC 000001.10:g.216363723AAGA[8]
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Gene symbol:Gene id.	USH2A:7399
Molecular consequence	SO:0001627|intron variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000155428; RCV000304777; RCV000399208; RCV001519720; RCV003445588; RCV003445589;
Chromosome	1:216363722..216363725
ClinVar Allele ID	172769
Disease database name and identifier	MedGen:CN239466|MedGen:CN169374|MedGen:C3661900|MONDO:MONDO:0010775, MedGen:C5779620, OMIM:500004|MONDO:MONDO:0013436, MedGen:C3151138, OMIM:613809, Orphanet:791|MONDO:MONDO:0010169, MedGen:C1848634, OMIM:276901, Orphanet:231178, Orphanet:886
ClinVar preferred disease name	Retinitis Pigmentosa, Recessive|not specified|not provided|Retinitis pigmentosa-deafness syndrome|Retinitis pigmentosa 39|Usher syndrome type 2A
HGVS variant names	NC 000001.10:g.216363723AAGA[5]
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Benign/Likely benign
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Variant clinical sources reported	ClinGen:CA182761
Gene symbol:Gene id.	USH2A:7399
Molecular consequence	SO:0001627|intron variant
Allele origin	germline
dbSNP ID	372388546
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002209901;
Chromosome	1:216363722..216363729
ClinVar Allele ID	1622836
Disease database name and identifier	MedGen:C3661900
ClinVar preferred disease name	not provided
HGVS variant names	NC 000001.10:g.216363723AAGA[4]
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Gene symbol:Gene id.	USH2A:7399
Molecular consequence	SO:0001627|intron variant
Allele origin	germline
dbSNP ID	372388546
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