View genomic variant #0000015565

Chromosome	1
Allele	Unknown
Affects function (as reported)	Probably does not affect function
Affects function (by curator)	Probably does not affect function
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.161169165G>T
Published as	-
GERP	-
Segregation	-
DB-ID	NDUFS2_000042
MSCV	MSCV_0015565
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

4 entries on 1 page. Showing entries 1 - 4.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
NDUFS2	00000209	NM_001166159.1	0000015565	./.	-	-	c.-3011G>T	p.(=)	-	-	-	-
NDUFS2	00000208	NM_004550.4	0000015565	./.	-	-	c.-388G>T	p.(=)	-	-	-	-
NDUFS2	00000207	XM_005245208.1	0000015565	./.	-	-	c.-240+1888G>T	p.(=)	-	-	-	-
NDUFS2	00000210	XM_005245209.1	0000015565	./.	-	-	c.-3198G>T	p.(=)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000278644;
Chromosome	1:161169165..161169165
ClinVar Allele ID	277868
Disease database name and identifier	MONDO:MONDO:0100224, MedGen:CN257533, OMIM:252010
ClinVar preferred disease name	Mitochondrial complex I deficiency, nuclear type 1
HGVS variant names	NC 000001.10:g.161169165G>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA10608511
Gene symbol:Gene id.	NDUFS2:4720
Molecular consequence	SO:0001623\|5 prime UTR variant, SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	3813623
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000336009; RCV001610796; RCV003343753;
Chromosome 1:161169165..161169165
Allele frequencies from TGP 0.15895
ClinVar Allele ID 277920
Disease database name and identifier MONDO:MONDO:0100224, MedGen:CN257533, OMIM:252010|MONDO:MONDO:0032611, MedGen:C4748759, OMIM:618228|MedGen:C3661900
ClinVar preferred disease name Mitochondrial complex I deficiency, nuclear type 1|Mitochondrial complex 1 deficiency, nuclear type 6|not provided
HGVS variant names NC 000001.10:g.161169165G>T
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:CA10608534
Gene symbol:Gene id. NDUFS2:4720
Molecular consequence SO:0001623|5 prime UTR variant, SO:0001627|intron variant
Allele origin germline
dbSNP ID 3813623
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