View genomic variant #0000000956

Chromosome	3
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.128628894C>T
Published as	-
GERP	1.830
Segregation	-
DB-ID	ACAD9_000004 See all 2 reported entries
MSCV	MSCV_0000956
dbSNP ID	rs377022708
Frequency	-
Sources	; clinVar;
Reference	21057504;22499348
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	8.0E-5 View details
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.

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

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.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	Protein	PolyPhen	GVS function	Splice distance	SIFT
ACAD9	00000014	NM_014049.4	0000000956	+/+	-	16/18	c.1594C>T	-	p.(Arg532Trp)	probably_damaging(0.995)	missense_variant	-	deleterious(0)
ACAD9	00000015	NR_033426.1	0000000956	+/+	-	16/18	n.1972C>T	-	-	-	non_coding_transcript_exon_variant,non_coding_transcript_variant	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000023869; RCV000200123; RCV001844016;
Chromosome	3:128628894..128628894
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00001
ClinVar Allele ID	39841
Disease database name and identifier	MONDO:MONDO:0100133, MedGen:C1838979, Orphanet:2609\|MedGen:C3661900\|MONDO:MONDO:0012624, MedGen:C4747517, OMIM:611126, Orphanet:99901
ClinVar preferred disease name	Mitochondrial complex I deficiency\|not provided\|Acyl-CoA dehydrogenase 9 deficiency
HGVS variant names	NC 000003.11:g.128628894C>T
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA129521\|OMIM:611103.0006\|UniProtKB:Q9H845#VAR 071905
Gene symbol:Gene id.	ACAD9:28976\|CFAP92:57501
Molecular consequence	SO:0001583\|missense variant, SO:0001619\|non-coding transcript variant, SO:0001624\|3 prime UTR variant
Allele origin	germline
dbSNP ID	377022708
For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN	MONDO:MONDO:0012624, MedGen:C4747517, OMIM:611126, Orphanet:99901
For included Variant : ClinVar preferred disease name for the concept specified by disease identifiers in CLNDISDB	Acyl-CoA dehydrogenase 9 deficiency
Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance.	424746:Pathogenic
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV003466630;
Chromosome 3:128628895..128628895
ClinVar Allele ID 2835573
Disease database name and identifier MONDO:MONDO:0012624, MedGen:C4747517, OMIM:611126, Orphanet:99901
ClinVar preferred disease name Acyl-CoA dehydrogenase 9 deficiency
HGVS variant names NC 000003.11:g.128628897del
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. ACAD9:28976|CFAP92:57501
Molecular consequence SO:0001589|frameshift variant, SO:0001619|non-coding transcript variant, SO:0001624|3 prime UTR variant
Allele origin unknown
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