View genomic variant #0000025908

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.

Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:

• 5' gene flanking
• 5' UTR
• Exon
• Intron
• 3' UTR
• 3' gene flanking

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.

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.

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

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

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

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

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

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

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

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

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	RNA change	Protein	PolyPhen	GVS function	Splice distance	SIFT
BCS1L	00000013	NM_001079866.1	0000025908	./.	-	-	c.771del	-	r.(?)	p.(Asp258Thrfs*13)	-	-	-	-
BCS1L	00000012	NM_004328.4	0000025908	./.	-	-	c.771del	-	r.(?)	p.(Asp258Thrfs*13)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000670440; RCV001855542;
Chromosome	2:219527284..219527284
ClinVar Allele ID	541815
Disease database name and identifier	MedGen:CN517202|MONDO:MONDO:0011308, MedGen:C1864002, OMIM:603358, Orphanet:53693
ClinVar preferred disease name	not provided|GRACILE syndrome
HGVS variant names	NC 000002.11:g.219527285del
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Gene symbol:Gene id.	BCS1L:617
Molecular consequence	SO:0001589|frameshift variant, SO:0001619|non-coding transcript variant
Allele origin	germline
dbSNP ID	1363475546
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000438295; RCV001138380; RCV001138378; RCV001138379; RCV002521706;
Chromosome	2:219527284..219527284
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00007
ClinVar Allele ID	366991
Disease database name and identifier	MedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0011308, MedGen:C1864002, OMIM:603358, Orphanet:53693|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506|MONDO:MONDO:0007415, MedGen:C3541471, OMIM:124000, Orphanet:254902
ClinVar preferred disease name	not specified|not provided|GRACILE syndrome|Leigh syndrome|Mitochondrial complex III deficiency nuclear type 1
HGVS variant names	NC 000002.11:g.219527284G>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(3)|Likely benign(2)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA2109755
Gene symbol:Gene id.	BCS1L:617
Molecular consequence	SO:0001619|non-coding transcript variant, SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	148302981
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