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 -
Average frequency (large NGS studies) 0.00138 View details
Owner LOVD

Variant on transcripts

1 entry on 1 page. Showing entry 1.


Transcript ID     


Variant ID     

Affects function     



DNA change (cDNA)     



GVS function     

Splice distance     

CPT2 00000665 NM_000098.2 0000000024 +/+ - 3/5 c.338C>T p.(Ser113Leu) probably_damaging(0.98) missense_variant,splice_region_variant - deleterious(0)

ClinVar @ MSeqDR

RCVaccession RCV000202499; RCV000515252; RCV000576571; RCV000194764; RCV000515252; RCV000009510; RCV000515252; RCV000515252; RCV000624845; RCV000185836;
Chromosome 1:53668099..53668099
Allele frequencies from ESP 0.0014
Allele frequencies from ExAC 0.00127
Allele frequencies from TGP 0.0006
ClinVar Allele ID 23992
Disease database name and identifier MeSH:D030342, MedGen:C0950123|MedGen:C0342790, Orphanet:ORPHA157, SNOMED CT:238002005|MedGen:C1833508, OMIM:255110, Orphanet:ORPHA228302|MedGen:C1833511, OMIM:600649, Orphanet:ORPHA228305|MedGen:C1833518, OMIM:608836, Orphanet:ORPHA228308|MedGen:C3280160, OMIM:614212, Orphanet:ORPHA263524|MedGen:CN517202
ClinVar preferred disease name Inborn genetic diseases|Carnitine palmitoyltransferase II deficiency|Carnitine palmitoyltransferase II deficiency, myopathic, stress-induced|Carnitine palmitoyltransferase II deficiency, infantile|Carnitine palmitoyltransferase II deficiency, lethal neonatal|Encephalopathy, acute, infection-induced, 4, susceptibility to|not provided
HGVS variant names NC 000001.10:g.53668099C>T
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported HGMD:CM930171|Illumina Clinical Services Laboratory, Illumina:84620|OMIM Allelic Variant:600650.0002|UniProtKB (protein):P23786#VAR 001392
Gene symbol:Gene id. CPT2:1376
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 74315294
Variant Flags

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:


Ensembl Variant Phenotype Information:

rs7431529415366809953668099C/TT0.0009OMIM phenotype variantsCARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, LATE-ONSET
rs7431529415366809953668099C/TT0.0009OMIM phenotype variantsCarnitine palmitoyltransferase 2 deficiency late-onset
CM93017115366809953668099HGMD_MUTATIONHGMD-PUBLIC variantsAnnotated by HGMD but no phenotype description is publicly available