NM_000098.3:c.985G>T
Variant summary
Our verdict is Uncertain significance. The variant received 5 ACMG points: 6P and 1B. PM1PM2PP3_ModerateBP6
The NM_000098.3(CPT2):c.985G>T(p.Asp329Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000098.3 missense
Scores
Clinical Significance
Conservation
Publications
- carnitine palmitoyltransferase II deficiencyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Myriad Women’s Health
- carnitine palmitoyl transferase II deficiency, myopathic formInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia
- carnitine palmitoyl transferase II deficiency, neonatal formInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia
- carnitine palmitoyl transferase II deficiency, severe infantile formInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet
- encephalopathy, acute, infection-induced, susceptibility to, 4Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Uncertain_significance. The variant received 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT2 | NM_000098.3 | c.985G>T | p.Asp329Tyr | missense_variant | Exon 4 of 5 | ENST00000371486.4 | NP_000089.1 | |
CPT2 | NM_001330589.2 | c.985G>T | p.Asp329Tyr | missense_variant | Exon 4 of 5 | NP_001317518.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000398 AC: 10AN: 251210 AF XY: 0.0000663 show subpopulations
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727232 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Carnitine palmitoyltransferase II deficiency Uncertain:1Benign:1
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Inborn genetic diseases Uncertain:1
The c.985G>T (p.D329Y) alteration is located in exon 4 (coding exon 4) of the CPT2 gene. This alteration results from a G to T substitution at nucleotide position 985, causing the aspartic acid (D) at amino acid position 329 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at