View genomic variant #0000000024

Chromosome	1
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.53668099C>T
Published as	-
GERP	5.880
Segregation	-
DB-ID	CPT2_000012 See all 2 reported entries
MSCV	MSCV_0000024
dbSNP ID	rs74315294
Frequency	-
Sources	; clinvar; ensembl;
Reference	10398215;8786066;8358442;8651281;23757202;736528
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	0.00138 View details
Owner	LOVD

Variant on transcripts

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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.

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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	0000000024	+/+	-	3/5	c.338C>T	p.(Ser113Leu)	probably_damaging(0.98)	missense_variant,splice_region_variant	-	deleterious(0)

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ClinVar @ MSeqDR
RCVaccession	RCV000009510; RCV000194764; RCV000185836; RCV000202499; RCV000515252; RCV000576571; RCV000624845; RCV000662284; RCV001004157; RCV001813968; RCV003137507;
Chromosome	1:53668099..53668099
Allele frequencies from ESP	0.00138
Allele frequencies from ExAC	0.00127
Allele frequencies from TGP	0.00060
ClinVar Allele ID	23992
Disease database name and identifier	Human Phenotype Ontology:HP:0003201, MedGen:C0035410\|MONDO:MONDO:0010914, MedGen:C1833511, OMIM:600649, Orphanet:228305\|MONDO:MONDO:0009704, MedGen:C1833508, OMIM:255110, Orphanet:157, Orphanet:228302\|MONDO:MONDO:0013633, MedGen:C3280160, OMIM:614212, Orphanet:263524\|MONDO:MONDO:0012136, MedGen:C1833518, OMIM:608836, Orphanet:228308\|MeSH:D030342, MedGen:C0950123\|MONDO:MONDO:0015515, MedGen:C0342790, Orphanet:157\|MedGen:C3661900\|Human Phenotype Ontology:HP:0003011, Human Phenotype Ontology:HP:0003197, Human Phenotype Ontology:HP:0003708, MedGen:C4021745
ClinVar preferred disease name	Rhabdomyolysis\|Carnitine palmitoyl transferase II deficiency, severe infantile form\|Carnitine palmitoyl transferase II deficiency, myopathic form\|Encephalopathy, acute, infection-induced, susceptibility to, 4\|Carnitine palmitoyl transferase II deficiency, neonatal form\|Inborn genetic diseases\|Carnitine palmitoyltransferase II deficiency\|not provided\|Abnormality of the musculature
HGVS variant names	NC 000001.10:g.53668099C>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Pathogenic(31)\|Likely pathogenic(2)\|Uncertain significance(1)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA254605\|Genetic Testing Registry (GTR):GTR000604056\|OMIM:600650.0002\|UniProtKB:P23786#VAR 001392
Gene symbol:Gene id.	CPT2:1376
Molecular consequence	SO:0001583\|missense variant
Allele origin
dbSNP ID	74315294
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