View genomic variant #0000019359

Variant on transcripts

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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
NDUFS1	00000204	NM_001199981.1	0000019359	./.	-	-	c.1285-7del	p.(=)	-	-	-	-
NDUFS1	00000202	NM_001199982.1	0000019359	./.	-	-	c.1060-7del	p.(=)	-	-	-	-
NDUFS1	00000203	NM_001199983.1	0000019359	./.	-	-	c.1222-7del	p.(=)	-	-	-	-
NDUFS1	00000206	NM_001199984.1	0000019359	./.	-	-	c.1435-7del	p.(=)	-	-	-	-
NDUFS1	00000205	NM_005006.6	0000019359	./.	-	-	c.1393-7del	p.(=)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000313581; RCV000352020; RCV001519149;
Chromosome	2:206997836..206997836
ClinVar Allele ID	287238
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.206997846del
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:CA2070449
Gene symbol:Gene id.	NDUFS1:4719
Molecular consequence	SO:0001627|intron variant
Allele origin	germline
dbSNP ID	760292289
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001141371; RCV001141370; RCV001510839;
Chromosome	2:206997836..206997836
Allele frequencies from ExAC	0.00374
Allele frequencies from TGP	0.00160
ClinVar Allele ID	887243
Disease database name and identifier	MONDO:MONDO:0100224, MedGen:CN257533, OMIM:252010|MedGen:CN517202|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506
ClinVar preferred disease name	Mitochondrial complex I deficiency, nuclear type 1|not provided|Leigh syndrome
HGVS variant names	NC 000002.11:g.206997836A>T
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Benign/Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	NDUFS1:4719
Molecular consequence	SO:0001627|intron variant
Allele origin	germline
dbSNP ID	200409285
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