CYP2S1

cytochrome P450 family 2 subfamily S member 1, the group of Cytochrome P450 family 2

Basic information

Region (hg38): 19:41193209-41207539

Links

ENSG00000167600 ∙ NCBI:29785 ∙ OMIM:611529 ∙ HGNC:15654 ∙ Uniprot:Q96SQ9 ∙ 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 CYP2S1 gene.

• Inborn genetic diseases (25 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP2S1 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	2	4
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	2

Variants in CYP2S1

This is a list of pathogenic ClinVar variants found in the CYP2S1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41193277-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-41193287-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-41193319-C-A		not specified	Uncertain significance (Aug 17, 2021)
19-41193335-C-T		not specified	Uncertain significance (May 25, 2022)
19-41194544-C-T		not specified	Likely benign (Dec 28, 2023)
19-41194563-C-T		not specified	Uncertain significance (Jun 26, 2023)
19-41194565-G-T		not specified	Uncertain significance (Oct 27, 2022)
19-41194592-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-41194664-G-A		not specified	Uncertain significance (May 11, 2022)
19-41194668-G-A		not specified	Uncertain significance (May 23, 2023)
19-41197844-G-A		not specified	Uncertain significance (Oct 05, 2022)
19-41197858-G-A			Benign (Dec 28, 2017)
19-41197863-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-41197865-G-C		not specified	Uncertain significance (Oct 10, 2023)
19-41197871-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-41197905-T-C		not specified	Uncertain significance (Jul 12, 2023)
19-41198491-G-C		not specified	Uncertain significance (Oct 07, 2022)
19-41198575-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-41198825-G-C			Likely benign (Jul 01, 2022)
19-41198829-C-G		not specified	Uncertain significance (Mar 02, 2023)
19-41198836-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-41201307-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-41201330-G-A		not specified	Uncertain significance (Jul 28, 2021)
19-41201343-T-C		not specified	Uncertain significance (Aug 22, 2023)
19-41203461-G-C		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP2S1	protein_coding	protein_coding	ENST00000310054	9	14491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000481	0.968	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	260	305	0.851	0.0000196	3175
Missense in Polyphen		81	108.29	0.74801		1206
Synonymous	0.654	127	137	0.929	0.00000854	1138
Loss of Function	1.94	10	19.1	0.522	9.68e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00229	0.00228
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a potential importance for extrahepatic xenobiotic metabolism.
• Pathway: Retinol metabolism - Homo sapiens (human);nicotine degradation III;Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Vitamin D Receptor Pathway;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;bupropion degradation;acetone degradation I (to methylglyoxal);Xenobiotics;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Miscellaneous substrates;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;superpathway of tryptophan utilization;CYP2E1 reactions;melatonin degradation I;superpathway of melatonin degradation;Arachidonic acid metabolism;nicotine degradation IV (Consensus)

Intolerance Scores

• loftool: 0.562
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.48

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.241

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp2s1
• Phenotype: normal phenotype

Gene ontology

• Biological process: organic acid metabolic process;xenobiotic metabolic process;epoxygenase P450 pathway;exogenous drug catabolic process;oxidation-reduction process
• Cellular component: cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: iron ion binding;protein binding;arachidonic acid epoxygenase activity;steroid hydroxylase activity;retinoic acid 4-hydroxylase activity;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;heme binding;aromatase activity