View genomic variant #0000015506

Chromosome	1
Allele	Unknown
Affects function (as reported)	Not classified
Affects function (by curator)	Not classified
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.119575820del
Published as	-
GERP	-
Segregation	-
DB-ID	WARS2_000004
MSCV	MSCV_0015506
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
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.

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.

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

5 entries on 1 page. Showing entries 1 - 5.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
WARS2	00001295	NM_015836.3	0000015506	./.	-	-	c.797del	p.(Pro266Argfs*10)	-	-	-	-
WARS2	00001296	NM_201263.2	0000015506	./.	-	-	c.*163del	p.(=)	-	-	-	-
WARS2	00001297	XM_005270350.1	0000015506	./.	-	-	c.743del	p.(Pro248Argfs*10)	-	-	-	-
WARS2	00001294	XM_005270351.1	0000015506	./.	-	-	c.626del	p.(Pro209Argfs*10)	-	-	-	-
WARS2	00001293	XM_005270352.1	0000015506	./.	-	-	c.*132del	p.(=)	-	-	-	-

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ClinVar @ MSeqDR
RCVaccession	RCV000509079; RCV000624348; RCV001821423; RCV003147494;
Chromosome	1:119575820..119575820
ClinVar Allele ID	434546
Disease database name and identifier	MONDO:MONDO:0060578, MedGen:C4540192, OMIM:617710, Orphanet:572798\|MedGen:CN517202\|MeSH:D030342, MedGen:C0950123\|MONDO:MONDO:0030676, MedGen:C5676913, OMIM:619738
ClinVar preferred disease name	Neurodevelopmental disorder, mitochondrial, with abnormal movements and lactic acidosis, with or without seizures\|not provided\|Inborn genetic diseases\|Parkinsonism-dystonia 3, childhood-onset
HGVS variant names	NC 000001.10:g.119575822del
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Likely pathogenic(4)\|Uncertain significance(2)
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Variant clinical sources reported	ClinGen:CA1035219\|OMIM:604733.0005
Gene symbol:Gene id.	WARS2:10352
Molecular consequence	SO:0001589\|frameshift variant, SO:0001624\|3 prime UTR variant
Allele origin	germline
dbSNP ID	746478253
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV001823668; RCV002542744;
Chromosome 1:119575820..119575820
Allele frequencies from ESP 0.00008
Allele frequencies from ExAC 0.00002
ClinVar Allele ID 1330256
Disease database name and identifier MONDO:MONDO:0060578, MedGen:C4540192, OMIM:617710, Orphanet:572798|MedGen:C3661900
ClinVar preferred disease name Neurodevelopmental disorder, mitochondrial, with abnormal movements and lactic acidosis, with or without seizures|not provided
HGVS variant names NC 000001.10:g.119575820G>A
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Uncertain significance
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Gene symbol:Gene id. WARS2:10352
Molecular consequence SO:0001583|missense variant, SO:0001624|3 prime UTR variant
Allele origin germline
dbSNP ID 368914534
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