CYP2S1

protein-coding

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

Gene summary

This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum. In rodents, the homologous protein has been shown to metabolize certain carcinogens; however, the specific function of the human protein has not been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_030622.8

Inheritance

—

ClinVar variants

U:83B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr19:41,193,210-41,207,539

External References & Databases

Ensembl (ENSG00000167600)

Transcript & Mutation Effects

hg38 • Region Span ~14.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CYP2S1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030622.8. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	2 clinvar	6
missense			80 clinvar	5 clinvar		85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	83	8	2	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030622.8	RefSeq	NP_085125.1	9	MANE Select
ENST00000310054.9	Ensembl	ENSP00000308032.3	9	MANE Select
ENST00000593545.5	Ensembl	ENSP00000472555.1	4	Standard
ENST00000593890.1	Ensembl	ENSP00000469850.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

organic acid metabolic process
xenobiotic metabolic process
epoxygenase P450 pathway
exogenous drug catabolic process
oxidation-reduction process

Molecular Function

iron ion binding
protein binding
arachidonic acid epoxygenase activity
steroid hydroxylase activity
retinoic acid 4-hydroxylase activity

Cellular Component

cytoplasm
endoplasmic reticulum
endoplasmic reticulum membrane
organelle membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310054
Coding exons: 9
Length: 14491
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125748
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.922	260	305	0.851	0.0000196	3175
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.0023	0.0023	notable
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00016	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has a potential importance for extrahepatic xenobiotic metabolism.;

Intolerance Scores

LoFtool: 0.562
RVIS EVS: 0.05
RVIS percentile EVS: 57.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.208

Gene Damage Prediction

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