View genomic variant #0000021316

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

2 entries on 1 page. Showing entries 1 - 2.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
NDUFS4	00000213	NM_002495.2	0000021316	./.	-	-	c.470_471del	p.(Ser157*)	-	-	-	-
NDUFS4	00000212	XM_005248525.1	0000021316	./.	-	-	c.*33_*34del	p.(=)	-	-	-	-

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000578386;
Chromosome	5:52978993..52978994
ClinVar Allele ID	481428
Disease database name and identifier	MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506
ClinVar preferred disease name	Leigh syndrome
HGVS variant names	NC 000005.9:g.52978993 52978994del
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Variant clinical sources reported	ClinGen:CA658683384
Gene symbol:Gene id.	NDUFS4:4724
Molecular consequence	SO:0001587|nonsense, SO:0001619|non-coding transcript variant, SO:0001624|3 prime UTR variant
Allele origin	inherited
dbSNP ID	1554062427
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001193078; RCV003469307;
Chromosome	5:52978993..52978994
ClinVar Allele ID	916955
Disease database name and identifier	MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506|MONDO:MONDO:0100224, MedGen:CN257533, OMIM:252010
ClinVar preferred disease name	Leigh syndrome|Mitochondrial complex I deficiency, nuclear type 1
HGVS variant names	NC 000005.9:g.52978995 52978999dup
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Likely pathogenic
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	NDUFS4:4724
Molecular consequence	SO:0001589|frameshift variant, SO:0001619|non-coding transcript variant, SO:0001624|3 prime UTR variant
Allele origin	germline
dbSNP ID	1740730588
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