rs917744011
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000098.3(CPT2):c.98del(p.Gln33ArgfsTer40) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,538,348 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000065 ( 0 hom. )
Consequence
CPT2
NM_000098.3 frameshift
NM_000098.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.85
Genes affected
CPT2 (HGNC:2330): (carnitine palmitoyltransferase 2) The protein encoded by this gene is a nuclear protein which is transported to the mitochondrial inner membrane. Together with carnitine palmitoyltransferase I, the encoded protein oxidizes long-chain fatty acids in the mitochondria. Defects in this gene are associated with mitochondrial long-chain fatty-acid (LCFA) oxidation disorders. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 123 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-53197040-CA-C is Pathogenic according to our data. Variant chr1-53197040-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 495549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT2 | NM_000098.3 | c.98del | p.Gln33ArgfsTer40 | frameshift_variant | 1/5 | ENST00000371486.4 | |
CPT2 | NM_001330589.2 | c.98del | p.Gln33ArgfsTer40 | frameshift_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT2 | ENST00000371486.4 | c.98del | p.Gln33ArgfsTer40 | frameshift_variant | 1/5 | 1 | NM_000098.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000763 AC: 1AN: 131108Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 71654
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GnomAD4 exome AF: 0.00000649 AC: 9AN: 1386182Hom.: 0 Cov.: 30 AF XY: 0.00000731 AC XY: 5AN XY: 684180
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Carnitine palmitoyltransferase II deficiency Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 495549). This premature translational stop signal has been observed in individual(s) with clinical features of CPT2 deficiency (PMID: 21913903). This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Gln33Argfs*40) in the CPT2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPT2 are known to be pathogenic (PMID: 16781677, 16996287). - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 23, 2016 | Variant summary: The c.98delA (p.Gln33Argfs) variant in CPT2 gene is a frameshift change that results in the loss of the 589 amino acids of CPT (~90%). This change is predicted to cause loss of normal protein function through protein truncation or nonsense-mediated mRNA decay. The variant is absent from the large control population dataset of ExAC, but has been reported in at least 1 severely affected individual in compound heterozygosity with a known pathogenic variant (p.S113L) via published report. Taking together, the variant was classified as Pathogenic. - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Carnitine palmitoyl transferase II deficiency, severe infantile form Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Likely pathogenic, no assertion criteria provided | clinical testing | Counsyl | Jul 28, 2015 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 03, 2022 | Not observed at a significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30957255, 21913903) - |
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jul 11, 2022 | PP4, PM2, PM3, PVS1 - |
Carnitine palmitoyl transferase II deficiency, myopathic form;C1833511:Carnitine palmitoyl transferase II deficiency, severe infantile form;C1833518:Carnitine palmitoyl transferase II deficiency, neonatal form;C3280160:Encephalopathy, acute, infection-induced, susceptibility to, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 16, 2021 | - - |
Encephalopathy, acute, infection-induced, susceptibility to, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 04, 2023 | - - |
Carnitine palmitoyl transferase II deficiency, severe infantile form;C1833518:Carnitine palmitoyl transferase II deficiency, neonatal form Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | New York Genome Center | Sep 29, 2022 | The inherited variant c.98del in CPT2 has previously been reported in individuals with Carnitine Palmitoyltransferase II Deficiency [PMID: 21913903, 30957255] and has been deposited in ClinVar [ClinVar ID: 495549] as Pathogenic/Likely Pathogenic. The c.98del variant is observed in 27 alleles with 0 homozygotes in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.98del variant in CPT2 is located in exon 1 of this 5-exon gene, predicted to incorporate a premature termination codon (p.(Gln33ArgfsTer40)), and is expected to result in loss-of-function via nonsense mediated decay. Multiple loss-of-function variants that are downstream to the c.98del variant have been reported in the literature [PMID: 20301431] in individuals with Carnitine Palmitoyltransferase II Deficiency. Based on available evidence, this inherited c.98del p.(Gln33ArgfsTer40) variant identified in CPT2 is classified as Pathogenic. - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at