View genomic variant #0000001679

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.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

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	0000001679	+/+	c.2234C>T	p.(Thr745Met)	missense_variant	-	7/12	probably_damaging(1)	r.(?)	tolerated(0.06)

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001250602;
Chromosome	1:197396689..197396689
ClinVar Allele ID	962206
Disease database name and identifier	MONDO:MONDO:0013453, MedGen:C3151202, OMIM:613835, Orphanet:65
ClinVar preferred disease name	Leber congenital amaurosis 8
HGVS variant names	NC 000001.10:g.197396689C>G
ClinVar review status	no assertion criteria provided
Clinical Significance	Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	CRB1:23418
Molecular consequence	SO:0001583|missense variant, SO:0001619|non-coding transcript variant, SO:0001627|intron variant
Allele origin	inherited
dbSNP ID	28939720
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000006087; RCV000086315; RCV000787576; RCV000809110; RCV001074789; RCV001196030; RCV001250601; RCV001257864; RCV001826422; RCV002496280;
Chromosome	1:197396689..197396689
Allele frequencies from ExAC	0.00008
ClinVar Allele ID	20772
Disease database name and identifier	MONDO:MONDO:0010818, MedGen:C1838647, OMIM:600105, Orphanet:791|MONDO:MONDO:0013453, MedGen:C3151202, OMIM:613835, Orphanet:65|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:0008246, MedGen:C1868310, OMIM:172870, Orphanet:251295|MedGen:C3661900|MONDO:MONDO:0018998, MeSH:D057130, MedGen:C0339527, OMIM:PS204000, Orphanet:65|MedGen:C0339526|Human Phenotype Ontology:HP:0000547, MONDO:MONDO:0019200, MeSH:D012174, MedGen:C0035334, OMIM:268000, OMIM:PS268000, Orphanet:791
ClinVar preferred disease name	Retinitis pigmentosa 12|Leber congenital amaurosis 8|Retinal dystrophy|Pigmented paravenous retinochoroidal atrophy|not provided|Leber congenital amaurosis|Autosomal recessive retinitis pigmentosa|Retinitis pigmentosa
HGVS variant names	NC 000001.10:g.197396689C>T
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:CA228003|OMIM:604210.0005|UniProtKB:P82279#VAR 011643
Gene symbol:Gene id.	CRB1:23418
Molecular consequence	SO:0001583|missense variant, SO:0001619|non-coding transcript variant, SO:0001627|intron variant
Allele origin
dbSNP ID	28939720
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