1-53210039-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_000098.3(CPT2):c.365C>T(p.Ser122Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S122S) has been classified as Likely benign.
Frequency
Consequence
NM_000098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CPT2 | NM_000098.3 | c.365C>T | p.Ser122Phe | missense_variant | Exon 4 of 5 | ENST00000371486.4 | NP_000089.1 | |
CPT2 | NM_001330589.2 | c.365C>T | p.Ser122Phe | missense_variant | Exon 4 of 5 | NP_001317518.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 151912Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251266Hom.: 0 AF XY: 0.000471 AC XY: 64AN XY: 135904
GnomAD4 exome AF: 0.000194 AC: 284AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.000224 AC XY: 163AN XY: 727200
GnomAD4 genome AF: 0.000197 AC: 30AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:3
Reported in a patient with acute necrotizing encephalopathy who also harbors a potentially disease-causing variant in the RANBP2 gene (Iyer et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 26010953, 32102593) -
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not specified Uncertain:1
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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 Uncertain:1
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Carnitine palmitoyltransferase II deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at