CYP27C1

cytochrome P450 family 27 subfamily C member 1, the group of Cytochrome P450 family 27

Basic information

Region (hg38): 2:127183832-127220313

Links

ENSG00000186684 ∙ NCBI:339761 ∙ ∙ HGNC:33480 ∙ Uniprot:Q4G0S4 ∙ 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 CYP27C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP27C1 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		1
missense			36	2	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	1

Variants in CYP27C1

This is a list of pathogenic ClinVar variants found in the CYP27C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-127187294-C-T		not specified	Uncertain significance (Nov 09, 2023)
2-127187305-C-T		not specified	Likely benign (Feb 15, 2023)
2-127187308-C-G		not specified	Uncertain significance (Jul 25, 2023)
2-127187309-C-G		not specified	Uncertain significance (Oct 30, 2023)
2-127187314-G-A			Benign (Mar 29, 2018)
2-127187332-T-G		not specified	Uncertain significance (Feb 19, 2025)
2-127187353-T-C		not specified	Uncertain significance (Jul 19, 2022)
2-127193120-G-A			Likely benign (Jun 01, 2022)
2-127193188-A-G		not specified	Uncertain significance (Jan 18, 2025)
2-127193194-T-G		not specified	Uncertain significance (Feb 21, 2024)
2-127193210-G-A		not specified	Uncertain significance (Aug 05, 2024)
2-127193228-G-A		not specified	Uncertain significance (Sep 14, 2021)
2-127193243-G-A		not specified	Uncertain significance (Nov 30, 2022)
2-127193251-T-C		not specified	Uncertain significance (Sep 06, 2022)
2-127193791-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-127193809-C-G		not specified	Uncertain significance (May 04, 2023)
2-127193820-A-C		not specified	Uncertain significance (Dec 30, 2024)
2-127193839-G-A		not specified	Uncertain significance (Jun 03, 2024)
2-127193845-T-C		not specified	Uncertain significance (Feb 27, 2025)
2-127195354-G-C		not specified	Uncertain significance (Feb 27, 2025)
2-127195368-G-A		not specified	Uncertain significance (Dec 05, 2024)
2-127195431-C-A		not specified	Uncertain significance (Mar 27, 2023)
2-127195431-C-T		not specified	Likely benign (Nov 21, 2024)
2-127195432-G-A		not specified	Uncertain significance (May 20, 2024)
2-127195441-T-C		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP27C1	protein_coding	protein_coding	ENST00000335247	7	35959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.20e-7	0.775	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.685	198	227	0.872	0.0000139	2417
Missense in Polyphen		82	101.59	0.80717		1099
Synonymous	0.427	87	92.2	0.943	0.00000571	754
Loss of Function	1.31	12	18.0	0.667	9.49e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000626	0.000626
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000272	0.000272
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conversion of all-trans retinol (also called vitamin A1, the precursor of 11-cis retinal) to 3,4- didehydroretinol (also called vitamin A2, the precursor of 11-cis 3,4-didehydroretinal). Also acts on all-trans retinal and all- trans retinoic acid. {ECO:0000269|PubMed:27059013}.
• Pathway: Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.607
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.379
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.300

Gene Damage Prediction

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

Gene ontology

• Biological process: retinol metabolic process;retinoic acid metabolic process;retinal metabolic process;oxidation-reduction process
• Cellular component: cellular_component;membrane;intracellular membrane-bounded organelle
• Molecular function: retinoic acid binding;monooxygenase activity;11-cis retinal binding;all-trans retinal binding;iron ion binding;heme binding;all-trans retinol 3,4-desaturase activity;all-trans retinal 3,4-desaturase activity;all-trans retinoic acid 3,4-desaturase activity;11-cis-retinal 3,4-desaturase activity;all-trans-retinol binding