CROT

carnitine O-octanoyltransferase

Basic information

Region (hg38): 7:87345663-87399794

Links

ENSG00000005469 ∙ NCBI:54677 ∙ OMIM:606090 ∙ HGNC:2366 ∙ Uniprot:Q9UKG9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CROT gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CROT gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			26	1	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	1	1

Variants in CROT

This is a list of pathogenic ClinVar variants found in the CROT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-87349103-G-A		not specified	Uncertain significance (Mar 27, 2023)
7-87349112-A-G		not specified	Uncertain significance (Apr 06, 2023)
7-87349159-T-A		not specified	Uncertain significance (May 02, 2023)
7-87361398-G-T			Benign (Apr 11, 2018)
7-87361457-T-C		not specified	Uncertain significance (Nov 21, 2022)
7-87361460-C-T		not specified	Uncertain significance (Jul 12, 2023)
7-87361505-G-T		not specified	Uncertain significance (Oct 12, 2022)
7-87361516-G-A		not specified	Uncertain significance (Jan 16, 2024)
7-87361557-G-C		not specified	Uncertain significance (Nov 21, 2022)
7-87361762-C-A		not specified	Uncertain significance (Oct 26, 2022)
7-87369468-C-A		not specified	Uncertain significance (Dec 14, 2021)
7-87375649-A-T		not specified	Uncertain significance (Apr 19, 2023)
7-87375687-G-A		not specified	Uncertain significance (Jun 22, 2021)
7-87375832-G-A		not specified	Uncertain significance (May 09, 2023)
7-87375853-A-C		not specified	Uncertain significance (Nov 18, 2022)
7-87375892-G-A		not specified	Uncertain significance (May 26, 2022)
7-87377392-G-A		not specified	Uncertain significance (Nov 10, 2021)
7-87381952-T-C		not specified	Uncertain significance (Dec 06, 2022)
7-87381958-G-A		not specified	Uncertain significance (May 15, 2023)
7-87381968-T-G		not specified	Uncertain significance (Mar 29, 2022)
7-87382066-A-G			Likely benign (Feb 08, 2018)
7-87382123-T-C		not specified	Likely benign (Oct 27, 2022)
7-87382131-G-A		not specified	Uncertain significance (Dec 27, 2023)
7-87382482-C-A		not specified	Uncertain significance (Oct 27, 2022)
7-87391639-G-A		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CROT	protein_coding	protein_coding	ENST00000419147	17	54115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.43e-25	0.00216	125122	2	623	125747	0.00249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00457	342	342	0.999	0.0000175	4182
Missense in Polyphen		116	118.64	0.97772		1409
Synonymous	0.807	104	115	0.904	0.00000573	1181
Loss of Function	0.612	40	44.4	0.901	0.00000274	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00590	0.00569
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000334	0.000326
Finnish	0.00356	0.00356
European (Non-Finnish)	0.00285	0.00283
Middle Eastern	0.000334	0.000326
South Asian	0.00276	0.00268
Other	0.00202	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-oxidation of fatty acids. The highest activity concerns the C6 to C10 chain length substrate. Converts the end product of pristanic acid beta oxidation, 4,8-dimethylnonanoyl- CoA, to its corresponding carnitine ester. {ECO:0000269|PubMed:10486279}.
• Pathway: Peroxisome - Homo sapiens (human);Beta Oxidation of Very Long Chain Fatty Acids;Oxidation of Branched Chain Fatty Acids;Adrenoleukodystrophy, X-linked;Carnitine-acylcarnitine translocase deficiency;Metabolism of lipids;Metabolism of proteins;Beta-oxidation of pristanoyl-CoA;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.113
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.16

Haploinsufficiency Scores

• pHI: 0.0880
• hipred: N
• hipred_score: 0.219
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.130

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Crot

Gene ontology

• Biological process: generation of precursor metabolites and energy;protein targeting to peroxisome;fatty acid metabolic process;fatty acid beta-oxidation;carnitine metabolic process;fatty acid transport;coenzyme A metabolic process;fatty acid beta-oxidation using acyl-CoA oxidase;medium-chain fatty acid metabolic process
• Cellular component: peroxisome;peroxisomal matrix;cytosol;intracellular membrane-bounded organelle
• Molecular function: signaling receptor binding;carnitine O-octanoyltransferase activity