chr7-87361516-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021151.4(CROT):c.367G>A(p.Glu123Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000343 in 1,459,764 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
CROT
NM_021151.4 missense
NM_021151.4 missense
Scores
2
10
5
Clinical Significance
Conservation
PhyloP100: 4.94
Genes affected
CROT (HGNC:2366): (carnitine O-octanoyltransferase) This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein converts 4,8-dimethylnonanoyl-CoA to its corresponding carnitine ester. This transesterification occurs in the peroxisome and is necessary for transport of medium- and long- chain acyl-CoA molecules out of the peroxisome to the cytosol and mitochondria. The protein thus plays a role in lipid metabolism and fatty acid beta-oxidation. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CROT | NM_021151.4 | c.367G>A | p.Glu123Lys | missense_variant | 5/18 | ENST00000331536.8 | |
CROT | NM_001143935.2 | c.451G>A | p.Glu151Lys | missense_variant | 6/19 | ||
CROT | XM_011516337.4 | c.367G>A | p.Glu123Lys | missense_variant | 5/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CROT | ENST00000331536.8 | c.367G>A | p.Glu123Lys | missense_variant | 5/18 | 1 | NM_021151.4 | P1 | |
CROT | ENST00000419147.6 | c.451G>A | p.Glu151Lys | missense_variant | 6/19 | 2 | |||
CROT | ENST00000442291.1 | c.367G>A | p.Glu123Lys | missense_variant | 4/17 | 5 | |||
CROT | ENST00000488850.1 | n.74G>A | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459764Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726174
GnomAD4 exome
AF:
AC:
5
AN:
1459764
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
726174
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.451G>A (p.E151K) alteration is located in exon 6 (coding exon 4) of the CROT gene. This alteration results from a G to A substitution at nucleotide position 451, causing the glutamic acid (E) at amino acid position 151 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
0.64
.;P;.
Vest4
MutPred
0.61
.;Gain of MoRF binding (P = 0.0074);Gain of MoRF binding (P = 0.0074);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.