CRAT

carnitine O-acetyltransferase

Basic information

Region (hg38): 9:129094142-129111189

Links

ENSG00000095321 ∙ NCBI:1384 ∙ OMIM:600184 ∙ HGNC:2342 ∙ Uniprot:P43155 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodegeneration with brain iron accumulation 8 (Limited), mode of inheritance: AR
• neurodegeneration with brain iron accumulation 8 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodegeneration with brain iron accumulation 8	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29395073

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRAT 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			2	47	5	54
missense			125	2	4	131
nonsense			1			1
start loss			1			1
frameshift			4			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)			3			3
splice region			7	3		10
non coding			1	23	4	28
Total	0	0	138	72	13

Variants in CRAT

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

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

Position	Type	Phenotype	Significance	ClinVar
9-129095407-G-GC		not specified	Uncertain significance (Mar 13, 2024)
9-129095408-C-G			Benign (Jan 30, 2024)
9-129095410-C-T		not specified	Uncertain significance (Apr 25, 2022)
9-129095410-CG-C			Uncertain significance (Apr 01, 2021)
9-129095411-G-A			Uncertain significance (May 18, 2022)
9-129095434-C-A			Benign (Dec 07, 2023)
9-129095434-C-T		not specified	Uncertain significance (Feb 22, 2023)
9-129095435-G-A			Uncertain significance (Oct 10, 2022)
9-129095437-A-G			Uncertain significance (Dec 02, 2021)
9-129095448-C-G			Likely benign (May 22, 2023)
9-129095458-A-G			Uncertain significance (Sep 09, 2022)
9-129095464-T-C		not specified	Uncertain significance (Apr 01, 2024)
9-129095467-G-A		not specified	Uncertain significance (Mar 13, 2024)
9-129095473-C-T		not specified	Uncertain significance (Jul 25, 2023)
9-129095480-C-T		not specified	Uncertain significance (Nov 23, 2023)
9-129095481-G-A		Neurodegeneration with brain iron accumulation 8	Benign/Likely benign (Dec 11, 2023)
9-129095486-T-C			Uncertain significance (Oct 22, 2022)
9-129095489-C-T		not specified	Uncertain significance (Oct 10, 2023)
9-129095491-G-A		not specified	Uncertain significance (Jan 19, 2022)
9-129095492-C-T			Uncertain significance (Nov 29, 2023)
9-129095493-G-A			Likely benign (Jan 22, 2024)
9-129095494-C-A		not specified	Uncertain significance (May 16, 2022)
9-129095501-T-C		not specified	Uncertain significance (Mar 25, 2024)
9-129095508-C-T			Uncertain significance (Aug 10, 2023)
9-129095509-G-A			Uncertain significance (Jul 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRAT	protein_coding	protein_coding	ENST00000318080	14	16380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.48e-12	0.704	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.852	354	402	0.880	0.0000260	4097
Missense in Polyphen		105	133.94	0.78395		1421
Synonymous	0.578	160	170	0.944	0.0000117	1225
Loss of Function	1.59	22	31.6	0.696	0.00000160	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.000499	0.000496
East Asian	0.000435	0.000435
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000435	0.000435
South Asian	0.000850	0.000850
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the reversible transfer of acyl groups from carnitine to coenzyme A (CoA) and regulates the acyl-CoA/CoA ratio. Also plays a crucial role in the transport of fatty acids for beta-oxidation. May be specific for short chain fatty acids. {ECO:0000305|PubMed:29395073}.
• 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;Fatty Acid Beta Oxidation;mitochondrial L-carnitine shuttle;Metabolism of lipids;Metabolism of proteins;Beta-oxidation of pristanoyl-CoA;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine (Consensus)

Recessive Scores

• pRec: 0.509

Intolerance Scores

• loftool: 0.189
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.24

Haploinsufficiency Scores

• pHI: 0.0986
• hipred: N
• hipred_score: 0.379
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crat
• Phenotype: growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: protein targeting to peroxisome;carnitine metabolic process, CoA-linked;fatty acid beta-oxidation using acyl-CoA oxidase
• Cellular component: mitochondrion;mitochondrial inner membrane;peroxisome;peroxisomal matrix;endoplasmic reticulum;cytosol
• Molecular function: carnitine O-acetyltransferase activity;signaling receptor binding