View genomic variant #0000015319

Chromosome	1
Allele	Unknown
Affects function (as reported)	Probably affects function
Affects function (by curator)	Probably affects function
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.53676691C>T
Published as	-
GERP	-
Segregation	-
DB-ID	CPT2_000027
MSCV	MSCV_0015319
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

1 entry on 1 page. Showing entry 1.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
CPT2	00000665	NM_000098.2	0000015319	./.	-	-	c.1345C>T	p.(Gln449*)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000409596; RCV000411103; RCV000411620; RCV002058839;
Chromosome	1:53676691..53676691
ClinVar Allele ID	357120
Disease database name and identifier	MedGen:C3661900\|MONDO:MONDO:0009704, MedGen:C1833508, OMIM:255110, Orphanet:157, Orphanet:228302\|MONDO:MONDO:0010914, MedGen:C1833511, OMIM:600649, Orphanet:228305\|MONDO:MONDO:0012136, MedGen:C1833518, OMIM:608836, Orphanet:228308
ClinVar preferred disease name	not provided\|Carnitine palmitoyl transferase II deficiency, myopathic form\|Carnitine palmitoyl transferase II deficiency, severe infantile form\|Carnitine palmitoyl transferase II deficiency, neonatal form
HGVS variant names	NC 000001.10:g.53676691C>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:CA16040765
Gene symbol:Gene id.	CPT2:1376
Molecular consequence	SO:0001587\|nonsense
Allele origin	germline
dbSNP ID	1057517492
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000409771; RCV000410775; RCV000412327; RCV000801602;
Chromosome 1:53676691..53676691
ClinVar Allele ID 357121
Disease database name and identifier MONDO:MONDO:0009704, MedGen:C1833508, OMIM:255110, Orphanet:157, Orphanet:228302|MONDO:MONDO:0010914, MedGen:C1833511, OMIM:600649, Orphanet:228305|MONDO:MONDO:0012136, MedGen:C1833518, OMIM:608836, Orphanet:228308|MONDO:MONDO:0015515, MedGen:C0342790, Orphanet:157
ClinVar preferred disease name Carnitine palmitoyl transferase II deficiency, myopathic form|Carnitine palmitoyl transferase II deficiency, severe infantile form|Carnitine palmitoyl transferase II deficiency, neonatal form|Carnitine palmitoyltransferase II deficiency
HGVS variant names NC 000001.10:g.53676691delinsTA
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic/Likely pathogenic
Variant type Indel
Sequence Ontology for variant type SO:1000032
Variant clinical sources reported ClinGen:CA16040766
Gene symbol:Gene id. CPT2:1376
Molecular consequence SO:0001587|nonsense
Allele origin germline
dbSNP ID 1057517525
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