View genomic variant #0000000104

Chromosome	1
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.197404292T>C
Published as	-
GERP	5.700
Segregation	-
DB-ID	CRB1_000003
MSCV	MSCV_0000104
dbSNP ID	rs62635659
Frequency	-
Sources	; clinvar; ensembl;
Reference	11389483
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	Variant not found in online data sets
Owner	LOVD

Variant on transcripts

Legend

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

1 entry on 1 page. Showing entry 1.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
CRB1	00003182	NM_201253.2	0000000104	+/+	c.3299T>C	p.(Ile1100Thr)	missense_variant	-	9/12	probably_damaging(0.942)	r.(?)	deleterious(0.01)

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ClinVar @ MSeqDR
RCVaccession	RCV000086339; RCV001857424; RCV002247492; RCV003453026; RCV003453027;
Chromosome	1:197404292..197404292
ClinVar Allele ID	105785
Disease database name and identifier	MONDO:MONDO:0013453, MedGen:C3151202, OMIM:613835, Orphanet:65\|MONDO:MONDO:0010818, MedGen:C1838647, OMIM:600105, Orphanet:791\|MedGen:C3661900\|MONDO:MONDO:0008246, MedGen:C1868310, OMIM:172870, Orphanet:251295
ClinVar preferred disease name	Leber congenital amaurosis 8\|Retinitis pigmentosa 12\|not provided\|Pigmented paravenous retinochoroidal atrophy
HGVS variant names	NC 000001.10:g.197404292T>C
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA228035\|UniProtKB:P82279#VAR 022973
Gene symbol:Gene id.	CRB1:23418
Molecular consequence	SO:0001583\|missense variant, SO:0001619\|non-coding transcript variant, SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	62635659
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000006088; RCV000086340; RCV002490326;
Chromosome 1:197404292..197404292
ClinVar Allele ID 20773
Disease database name and identifier MONDO:MONDO:0013453, MedGen:C3151202, OMIM:613835, Orphanet:65|MONDO:MONDO:0008246, MedGen:C1868310, OMIM:172870, Orphanet:251295|MONDO:MONDO:0010818, MedGen:C1838647, OMIM:600105, Orphanet:791|MedGen:CN517202
ClinVar preferred disease name Leber congenital amaurosis 8|Pigmented paravenous retinochoroidal atrophy|Retinitis pigmentosa 12|not provided
HGVS variant names NC 000001.10:g.197404292T>G
ClinVar review status criteria provided, single submitter
Clinical Significance Likely pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA117707|OMIM:604210.0006|UniProtKB:P82279#VAR 011648
Gene symbol:Gene id. CRB1:23418
Molecular consequence SO:0001583|missense variant, SO:0001619|non-coding transcript variant, SO:0001627|intron variant
Allele origin germline
dbSNP ID 62635659
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