CPT1B

carnitine palmitoyltransferase 1B

Basic information

Region (hg38): 22:50568860-50578465

Links

ENSG00000205560 ∙ NCBI:1375 ∙ OMIM:601987 ∙ HGNC:2329 ∙ Uniprot:Q92523 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inherited fatty acid metabolism disorder (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPT1B gene.

• Inborn genetic diseases (45 variants)
• not provided (6 variants)
• CPT1B-related condition (2 variants)
• High myopia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPT1B 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					3	3
missense			44	2		46
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	46	2	3

Variants in CPT1B

This is a list of pathogenic ClinVar variants found in the CPT1B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50569343-T-G		not specified	Uncertain significance (Dec 09, 2023)
22-50569347-G-C			Benign (Aug 16, 2018)
22-50569348-G-A		not specified	Uncertain significance (Aug 13, 2021)
22-50569369-T-C		not specified	Uncertain significance (Dec 07, 2021)
22-50569412-G-A		not specified	Uncertain significance (Jan 26, 2022)
22-50569577-G-A		not specified	Uncertain significance (May 05, 2023)
22-50570351-C-T		not specified	Uncertain significance (Aug 10, 2021)
22-50570363-TG-T		CPT1B-related disorder	Uncertain significance (Mar 09, 2023)
22-50570371-C-G		not specified	Uncertain significance (Feb 01, 2023)
22-50570881-C-T		CPT1B-related disorder	Likely benign (Sep 08, 2022)
22-50570914-C-G		not specified	Uncertain significance (Nov 17, 2022)
22-50570971-C-T		not specified	Uncertain significance (Mar 31, 2022)
22-50570977-T-C		not specified	Uncertain significance (Jan 04, 2024)
22-50570985-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-50571058-T-C		not specified	Benign/Likely benign (-)
22-50571165-G-A		not specified	Uncertain significance (Dec 14, 2023)
22-50571172-C-T		not specified	Uncertain significance (Sep 20, 2022)
22-50571216-C-T		not specified	Uncertain significance (Aug 28, 2023)
22-50571240-C-G		not specified	Uncertain significance (Nov 22, 2021)
22-50571288-C-T		not specified	Likely benign (Apr 13, 2023)
22-50571432-C-A		not specified	Uncertain significance (May 16, 2022)
22-50571443-G-C		not specified	Uncertain significance (Dec 03, 2021)
22-50571473-A-C		not specified	Uncertain significance (Feb 27, 2023)
22-50571509-C-T		not specified	Uncertain significance (Jun 29, 2022)
22-50572089-A-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPT1B	protein_coding	protein_coding	ENST00000360719	18	10610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-11	0.986	125637	1	107	125745	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	449	479	0.936	0.0000301	5077
Missense in Polyphen		106	120.19	0.88191		1210
Synonymous	0.251	181	185	0.977	0.0000116	1493
Loss of Function	2.44	24	40.8	0.588	0.00000190	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000796	0.000796
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000656	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000441	0.000431
Middle Eastern	0.000656	0.000653
South Asian	0.000692	0.000653
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Adipocytokine signaling pathway - Homo sapiens (human);Insulin resistance - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Fatty Acid Beta Oxidation;PPAR signaling pathway;Signal Transduction;mitochondrial L-carnitine shuttle;Metabolism of lipids;Import of palmitoyl-CoA into the mitochondrial matrix;Metabolism;Fatty acid metabolism;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

• pRec: 0.348

Intolerance Scores

• loftool: 0.0174
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.229
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpt1b
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: fatty acid beta-oxidation;carnitine shuttle;carnitine metabolic process;long-chain fatty acid transport
• Cellular component: mitochondrion;mitochondrial outer membrane;integral component of membrane
• Molecular function: carnitine O-palmitoyltransferase activity;protein binding