View genomic variant #0000025353

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

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.

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.

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

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

Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

• benign = Benign
• possiblyDamaging = Possibly damaging
• probablyDamaging = Probably damaging
• noPrediction = No prediction

RNA change: Description of variant at RNA level (following HGVS recommendations).

• r.123c>u
• r.? = unknown
• r.(?) = RNA not analysed but probably transcribed copy of DNA variant
• r.spl? = RNA not analysed but variant probably affects splicing
• r.(spl?) = RNA not analysed but variant may affect splicing
• r.0? = change expected to abolish transcription

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

5 entries on 1 page. Showing entries 1 - 5.

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	DNA change (cDNA)	Exon	Protein	GVS function	Position	PolyPhen	RNA change	Splice distance	SIFT
ACADVL	00000390	NM_000018.3	0000025353	./.	-	c.14_30del	-	p.(Met6Alafs*47)	-	-	-	r.(?)	-	-
ACADVL	00000391	NM_001033859.2	0000025353	./.	-	c.14_30del	-	p.(Met6Alafs*38)	-	-	-	r.(?)	-	-
ACADVL	00000388	NM_001270447.1	0000025353	./.	-	c.132-124_132-108del	-	p.(=)	-	-	-	r.(=)	-	-
ACADVL	00000389	NM_001270448.1	0000025353	./.	-	c.-290_-274del	-	p.(=)	-	-	-	r.(=)	-	-
DLG4	00003308	NM_001365.3	0000025353	./.	-	c.-1165_-1149del	-	p.(=)	-	-	-	r.(=)	-	-

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	RCV000667776;
Chromosome	17:7123317..7123333
ClinVar Allele ID	548616
Disease database name and identifier	MONDO:MONDO:0008723, MedGen:C3887523, OMIM:201475, Orphanet:26793
ClinVar preferred disease name	Very long chain acyl-CoA dehydrogenase deficiency
HGVS variant names	NC 000017.10:g.7123319 7123335del
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Gene symbol:Gene id.	DLG4:1742|ACADVL:37
Molecular consequence	SO:0001589|frameshift variant, SO:0001619|non-coding transcript variant, SO:0001623|5 prime UTR variant, SO:0001627|intron variant
Allele origin	unknown
dbSNP ID	1555527450
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001401665;
Chromosome	17:7123333..7123333
ClinVar Allele ID	1083503
Disease database name and identifier	MONDO:MONDO:0008723, MedGen:C3887523, OMIM:201475, Orphanet:26793
ClinVar preferred disease name	Very long chain acyl-CoA dehydrogenase deficiency
HGVS variant names	NC 000017.10:g.7123333G>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	DLG4:1742|ACADVL:37
Molecular consequence	SO:0001619|non-coding transcript variant, SO:0001623|5 prime UTR variant, SO:0001627|intron variant, SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	2142959363
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