CYP26A1

cytochrome P450 family 26 subfamily A member 1, the group of Cytochrome P450 family 26

Basic information

Region (hg38): 10:93073475-93077885

Links

ENSG00000095596 ∙ NCBI:1592 ∙ OMIM:602239 ∙ HGNC:2603 ∙ Uniprot:O43174 ∙ 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 CYP26A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP26A1 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				1	2	3
missense			26			26
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	2

Variants in CYP26A1

This is a list of pathogenic ClinVar variants found in the CYP26A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-93074020-A-G		not specified	Uncertain significance (Jan 10, 2022)
10-93074074-G-A		not specified	Uncertain significance (Aug 05, 2023)
10-93074077-C-T		not specified	Uncertain significance (Oct 20, 2023)
10-93074423-T-A		not specified	Uncertain significance (Oct 25, 2023)
10-93074433-C-A		not specified	Uncertain significance (May 08, 2024)
10-93074440-G-T		not specified	Uncertain significance (Apr 09, 2024)
10-93074468-G-T		not specified	Uncertain significance (Feb 07, 2023)
10-93074788-C-T		not specified	Uncertain significance (Sep 22, 2023)
10-93074796-C-T			Benign (Mar 30, 2018)
10-93074800-C-A		not specified	Uncertain significance (Mar 19, 2024)
10-93074800-C-T		not specified	Uncertain significance (Aug 11, 2022)
10-93074811-C-G			Benign/Likely benign (Mar 01, 2023)
10-93074836-G-A		not specified	Uncertain significance (Dec 20, 2021)
10-93074852-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-93074882-G-A		not specified	Uncertain significance (Jun 02, 2024)
10-93074909-A-G		not specified	Uncertain significance (Jan 11, 2023)
10-93074995-G-T		CYP26A1-related condition	Likely benign (Aug 01, 2024)
10-93075174-A-G		not specified	Uncertain significance (Dec 15, 2023)
10-93075184-C-G		not specified	Uncertain significance (Jan 31, 2022)
10-93075185-G-C		not specified	Uncertain significance (Dec 21, 2022)
10-93075201-C-G		not specified	Uncertain significance (Mar 31, 2024)
10-93075233-G-C		not specified	Uncertain significance (Mar 04, 2024)
10-93075238-G-C		not specified	Uncertain significance (Oct 20, 2021)
10-93075296-C-G		not specified	Uncertain significance (Jan 07, 2022)
10-93075818-A-G			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP26A1	protein_coding	protein_coding	ENST00000224356	7	4416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.43e-11	0.268	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.435	261	282	0.927	0.0000133	3216
Missense in Polyphen		119	126.12	0.94352		1469
Synonymous	-1.36	138	119	1.16	0.00000580	1013
Loss of Function	0.863	18	22.4	0.803	0.00000116	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000654	0.000651
Ashkenazi Jewish	0.00	0.00
East Asian	0.000630	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000110	0.000105
Middle Eastern	0.000630	0.000598
South Asian	0.000263	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a key role in retinoic acid metabolism. Acts on retinoids, including all-trans-retinoic acid (RA) and its stereoisomer 9-cis-RA. Capable of both 4-hydroxylation and 18- hydroxylation. Responsible for generation of several hydroxylated forms of RA, including 4-OH-RA, 4-oxo-RA and 18-OH-RA. {ECO:0000269|PubMed:9228017, ECO:0000269|PubMed:9716180}.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Adipogenesis;Nuclear Receptors in Lipid Metabolism and Toxicity;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Vitamin A and Carotenoid Metabolism;Signal Transduction;Phase I - Functionalization of compounds;RA biosynthesis pathway;Vitamins;Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;Vitamin A (retinol) metabolism;Signaling by Retinoic Acid;Signaling by Nuclear Receptors (Consensus)

Intolerance Scores

• loftool: 0.686
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.438
• hipred: Y
• hipred_score: 0.586
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp26a1
• Phenotype: skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail 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); reproductive system 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); normal phenotype; embryo phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: cyp26a1
• Affected structure: pectoral fin
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: kidney development;vitamin metabolic process;xenobiotic metabolic process;sterol metabolic process;response to retinoic acid;response to vitamin A;retinoic acid catabolic process;retinoic acid metabolic process;negative regulation of retinoic acid receptor signaling pathway;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;organelle membrane
• Molecular function: retinoic acid binding;iron ion binding;retinoic acid 4-hydroxylase activity;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen;oxygen binding;heme binding