View genomic variant #0000019381

Chromosome	2
Allele	Unknown
Affects function (as reported)	Not classified
Affects function (by curator)	Not classified
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.207014658_207014659del
Published as	-
GERP	-
Segregation	-
DB-ID	NDUFS1_000040
MSCV	MSCV_0019381
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.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
NDUFS1	00000204	NM_001199981.1	0000019381	./.	-	-	c.154-839_154-838del	p.(=)	-	-	-	-
NDUFS1	00000202	NM_001199982.1	0000019381	./.	-	-	c.6-2101_6-2100del	p.(=)	-	-	-	-
NDUFS1	00000203	NM_001199983.1	0000019381	./.	-	-	c.-18-10_-18-9del	p.(=)	-	-	-	-
NDUFS1	00000206	NM_001199984.1	0000019381	./.	-	-	c.196-10_196-9del	p.(=)	-	-	-	-
NDUFS1	00000205	NM_005006.6	0000019381	./.	-	-	c.154-10_154-9del	p.(=)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV001566492; RCV002506670;
Chromosome	2:207014657..207014658
ClinVar Allele ID	1189790
Disease database name and identifier	MedGen:C3661900\|MONDO:MONDO:0032610, MedGen:C4748754, OMIM:618226
ClinVar preferred disease name	not provided\|Mitochondrial complex 1 deficiency, nuclear type 5
HGVS variant names	NC 000002.11:g.207014682dup
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Benign/Likely benign
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	NDUFS1:4719
Molecular consequence	SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	568965659
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000959835;
Chromosome 2:207014657..207014658
ClinVar Allele ID 777232
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014677 207014682dup
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000953446;
Chromosome 2:207014657..207014658
ClinVar Allele ID 777235
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014668 207014682dup
ClinVar review status criteria provided, single submitter
Clinical Significance Likely benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000951062;
Chromosome 2:207014657..207014658
ClinVar Allele ID 777174
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014666 207014682dup
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000949250;
Chromosome 2:207014657..207014658
ClinVar Allele ID 777177
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014665 207014682dup
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000950385;
Chromosome 2:207014657..207014658
ClinVar Allele ID 777231
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014664 207014682dup
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000676279; RCV001700445; RCV002493117;
Chromosome 2:207014658..207014658
ClinVar Allele ID 549891
Disease database name and identifier MONDO:MONDO:0032610, MedGen:C4748754, OMIM:618226|MedGen:CN517202|MedGen:CN169374
ClinVar preferred disease name Mitochondrial complex 1 deficiency, nuclear type 5|not provided|not specified
HGVS variant names NC 000002.11:g.207014682del
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Likely benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000272442; RCV000329832; RCV000676276;
Chromosome 2:207014658..207014659
ClinVar Allele ID 284922
Disease database name and identifier MONDO:MONDO:0100133, MedGen:C1838979, Orphanet:2609|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506|MedGen:CN517202
ClinVar preferred disease name Mitochondrial complex I deficiency|Leigh syndrome|not provided
HGVS variant names NC 000002.11:g.207014681 207014682del
ClinVar review status criteria provided, conflicting interpretations
Clinical Significance Conflicting interpretations of pathogenicity
Conflicting clinical significance Uncertain significance(2)|Benign(1)
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Variant clinical sources reported ClinGen:CA2070864
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000306609; RCV000676277; RCV000999960;
Chromosome 2:207014658..207014660
ClinVar Allele ID 265866
Disease database name and identifier MedGen:CN517202|MONDO:MONDO:0032610, MedGen:C4748754, OMIM:618226|MedGen:CN169374
ClinVar preferred disease name not provided|Mitochondrial complex 1 deficiency, nuclear type 5|not specified
HGVS variant names NC 000002.11:g.207014680 207014682del
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:CA2070863
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000676278;
Chromosome 2:207014658..207014661
ClinVar Allele ID 549890
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014679 207014682del
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV001699730; RCV002503153;
Chromosome 2:207014658..207014662
ClinVar Allele ID 1274323
Disease database name and identifier MedGen:CN169374|MONDO:MONDO:0032610, MedGen:C4748754, OMIM:618226
ClinVar preferred disease name not specified|Mitochondrial complex 1 deficiency, nuclear type 5
HGVS variant names NC 000002.11:g.207014678 207014682del
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. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000958897;
Chromosome 2:207014658..207014663
ClinVar Allele ID 777223
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014677 207014682del
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000946664;
Chromosome 2:207014658..207014664
ClinVar Allele ID 777227
Disease database name and identifier MedGen:CN517202
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014676 207014682del
ClinVar review status criteria provided, single submitter
Clinical Significance Benign
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV002116759;
Chromosome 2:207014658..207014669
ClinVar Allele ID 1541947
Disease database name and identifier MedGen:C3661900
ClinVar preferred disease name not provided
HGVS variant names NC 000002.11:g.207014671 207014682del
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. NDUFS1:4719
Molecular consequence SO:0001627|intron variant
Allele origin germline
dbSNP ID 568965659
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