View genomic variant #0000000085

Chromosome	1
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	delins
DNA change (genomic) (Relative to hg19 / GRCh37)	g.173797450_173797451delinsC
Published as	-
GERP	-
Segregation	-
DB-ID	DARS2_000010
MSCV	MSCV_0000085
dbSNP ID	rs367543010
Frequency	-
Sources	; clinVar; Ensembl;
Reference	17384640;20506600;19592391
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

3 entries on 1 page. Showing entries 1 - 3.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
DARS2	00000091	NM_018122.4	0000000085	+/+	-	-	c.228-21_228-20delinsC	p.(=)	-	-	-	-
DARS2	00000089	XM_005245299.1	0000000085	+/+	-	-	c.69+1526_69+1527delinsC	p.(=)	-	-	-	-
DARS2	00000090	XM_005245300.1	0000000085	+/+	-	-	c.228-21_228-20delinsC	p.(=)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000023847;
Chromosome	1:173797449..173797449
ClinVar Allele ID	39819
Disease database name and identifier	MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898
ClinVar preferred disease name	Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome
HGVS variant names	NC 000001.10:g.173797449T>A
ClinVar review status	no assertion criteria provided
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	OMIM:610956.0012
Gene symbol:Gene id.	DARS2:55157
Molecular consequence	SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	1557853625
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000676385; RCV003343985;
Chromosome 1:173797450..173797451
Allele frequencies from TGP 0.00100
ClinVar Allele ID 549864
Disease database name and identifier MedGen:C3661900|MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898
ClinVar preferred disease name not provided|Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome
HGVS variant names NC 000001.10:g.173797450 173797451insC
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Benign/Likely benign
Variant type Insertion
Sequence Ontology for variant type SO:0000667
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 367543010
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000001112; RCV000415026; RCV000626945; RCV003332072;
Chromosome 1:173797450..173797451
ClinVar Allele ID 16096
Disease database name and identifier Human Phenotype Ontology:HP:0001368, Human Phenotype Ontology:HP:0001997, MONDO:MONDO:0005393, MedGen:C0018099|Human Phenotype Ontology:HP:0000822, Human Phenotype Ontology:HP:0004949, Human Phenotype Ontology:HP:0005126, MONDO:MONDO:0005044, MedGen:C0020538|Human Phenotype Ontology:HP:0001762, MONDO:MONDO:0007342, MedGen:C0009081, OMIM:119800, Orphanet:199315|Human Phenotype Ontology:HP:0003482, MedGen:C4025609|Human Phenotype Ontology:HP:0007222, Human Phenotype Ontology:HP:0007305, MedGen:C0338474|Human Phenotype Ontology:HP:0007055, Human Phenotype Ontology:HP:0007141, Human Phenotype Ontology:HP:0007237, MedGen:C1112256|Human Phenotype Ontology:HP:0002355, Human Phenotype Ontology:HP:0007101, Human Phenotype Ontology:HP:0009030, MedGen:C0311394|Human Phenotype Ontology:HP:0001760, Human Phenotype Ontology:HP:0010216, Human Phenotype Ontology:HP:0010611, MedGen:C5399834|Human Phenotype Ontology:HP:0002120, Human Phenotype Ontology:HP:0006823, Human Phenotype Ontology:HP:0006835, MedGen:C4551583|Human Phenotype Ontology:HP:0002166, MedGen:C1849134|MedGen:C3661900|MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898|Human Phenotype Ontology:HP:0002066, Human Phenotype Ontology:HP:0002379, MedGen:C0751837|Human Phenotype Ontology:HP:0001310, MedGen:C0234162|Human Phenotype Ontology:HP:0002141, Human Phenotype Ontology:HP:0100683, MedGen:C1836150
ClinVar preferred disease name Gout|Hypertensive disorder|Talipes equinovarus|EMG: axonal abnormality|CNS demyelination|Sensorimotor neuropathy|Difficulty walking|Abnormal foot morphology|Cerebral cortical atrophy|Impaired vibration sensation in the lower limbs|not provided|Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome|Gait ataxia|Dysmetria|Gait imbalance
HGVS variant names NC 000001.10:g.173797450 173797451delinsC
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic
Variant type Indel
Sequence Ontology for variant type SO:1000032
Variant clinical sources reported ClinGen:CA339865|OMIM:610956.0001
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 1553201258
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV003223928;
Chromosome 1:173797450..173797451
ClinVar Allele ID 2477815
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000001.10:g.173797450 173797451delinsCC
ClinVar review status criteria provided, single submitter
Clinical Significance Uncertain significance
Variant type Indel
Sequence Ontology for variant type SO:1000032
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV002866149;
Chromosome 1:173797451..173797453
ClinVar Allele ID 2079901
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000001.10:g.173797451 173797453del
ClinVar review status criteria provided, single submitter
Clinical Significance Likely benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000124657; RCV000676388; RCV003343652;
Chromosome 1:173797451..173797451
Allele frequencies from ExAC 0.24948
ClinVar Allele ID 140771
Disease database name and identifier MedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898
ClinVar preferred disease name not specified|not provided|Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome
HGVS variant names NC 000001.10:g.173797451T>C
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Benign
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA290566
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 55878143
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000605642;
Chromosome 1:173797451..173797451
ClinVar Allele ID 498284
Disease database name and identifier MedGen:CN169374
ClinVar preferred disease name not specified
HGVS variant names NC 000001.10:g.173797451delinsCC
ClinVar review status criteria provided, single submitter
Clinical Significance Likely benign
Variant type Indel
Sequence Ontology for variant type SO:1000032
Variant clinical sources reported ClinGen:CA658795565
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 1553201265
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000676391; RCV002489143;
Chromosome 1:173797451..173797452
ClinVar Allele ID 404985
Disease database name and identifier MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898|MedGen:C3661900
ClinVar preferred disease name Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome|not provided
HGVS variant names NC 000001.10:g.173797461dup
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Benign/Likely benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Variant clinical sources reported ClinGen:CA1250054
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 374122386
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV002130031;
Chromosome 1:173797451..173797452
ClinVar Allele ID 1557590
Disease database name and identifier MedGen:C3661900
ClinVar preferred disease name not provided
HGVS variant names NC 000001.10:g.173797460 173797461dup
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 374122386
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000676390; RCV003343852;
Chromosome 1:173797452..173797452
ClinVar Allele ID 404984
Disease database name and identifier MedGen:C3661900|MONDO:MONDO:0012622, MedGen:C1970180, OMIM:611105, Orphanet:137898
ClinVar preferred disease name not provided|Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome
HGVS variant names NC 000001.10:g.173797461del
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Variant clinical sources reported ClinGen:CA1250053
Gene symbol:Gene id. DARS2:55157
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 374122386
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