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PSORS1C1

gene
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Also known as SEEK1

Summary

PSORS1C1 (psoriasis susceptibility 1 candidate 1, HGNC:17202) is a protein-coding gene on chromosome 6p21.33, encoding Psoriasis susceptibility 1 candidate gene 1 protein (Q9UIG5).

This gene is one of several genes thought to confer susceptibility to psoriasis and systemic sclerosis, located on chromosome 6 near the major histocompatibility complex (MHC) class I region.

Source: NCBI Gene 170679 — RefSeq curated summary.

At a glance

  • GWAS associations: 94
  • Clinical variants (ClinVar): 52 total
  • MANE Select transcript: NM_014068

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17202
Approved symbolPSORS1C1
Namepsoriasis susceptibility 1 candidate 1
Location6p21.33
Locus typegene with protein product
StatusApproved
AliasesSEEK1
Ensembl geneENSG00000204540
Ensembl biotypeprotein_coding
OMIM613525
Entrez170679

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding_CDS_not_defined, 3 protein_coding, 2 retained_intron

ENST00000259881, ENST00000467107, ENST00000479581, ENST00000481450, ENST00000493289, ENST00000547221, ENST00000548049, ENST00000550838, ENST00000552747

RefSeq mRNA: 1 — MANE Select: NM_014068 NM_014068

CCDS: CCDS34390

Canonical transcript exons

ENST00000259881 — 6 exons

ExonStartEnd
ENSE000016669043113843031138459
ENSE000016976523112567631125839
ENSE000023840373113964131140092
ENSE000035201733112956931129645
ENSE000035429143113865631138779
ENSE000038939693111480031114891

Expression profiles

Bgee: expression breadth ubiquitous, 124 present calls, max score 97.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.7718 / max 96.8590, expressed in 938 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
668601.1633584
668591.0231582
668610.2213125
668580.199894
668620.125761
668660.02317
668650.01564

Top tissues by expression

132 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453397.21gold quality
right testisUBERON:000453497.09gold quality
testisUBERON:000047396.60gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.21gold quality
skin of legUBERON:000151187.54gold quality
zone of skinUBERON:000001486.62gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.58gold quality
skin of abdomenUBERON:000141685.50gold quality
lower esophagus mucosaUBERON:003583480.84gold quality
mucosa of stomachUBERON:000119980.63gold quality
descending thoracic aortaUBERON:000234579.50gold quality
ascending aortaUBERON:000149678.36gold quality
thoracic aortaUBERON:000151578.20gold quality
upper lobe of left lungUBERON:000895277.95gold quality
apex of heartUBERON:000209877.75gold quality
myometriumUBERON:000129677.47gold quality
vaginaUBERON:000099677.43gold quality
right lungUBERON:000216777.41gold quality
body of uterusUBERON:000985376.17gold quality
transverse colonUBERON:000115775.96gold quality
rectumUBERON:000105275.94gold quality
body of stomachUBERON:000116175.86gold quality
mucosa of transverse colonUBERON:000499175.63gold quality
metanephros cortexUBERON:001053375.44gold quality
small intestine Peyer’s patchUBERON:000345475.03gold quality
colonUBERON:000115574.59gold quality
duodenumUBERON:000211474.49gold quality
small intestineUBERON:000210874.37gold quality
muscle layer of sigmoid colonUBERON:003580574.15gold quality
tibial arteryUBERON:000761074.08gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting PSORS1C1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4673100.0066.641490
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-431899.3866.941505
HSA-MIR-4520-2-3P99.1469.281009
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-7851-3P98.7264.88980
HSA-MIR-7850-5P98.1267.281111
HSA-MIR-6730-5P98.0368.121299
HSA-MIR-61796.7965.96738
HSA-MIR-6742-5P96.3264.01869
HSA-MIR-6834-5P96.2564.88823

Literature-anchored findings (GeneRIF, showing 12)

  • In a case-control study, five of the nine single nucleotide polymorphisms (SNPs) found in SEEK1 were associated with psoriasis, while one of the four SNPs found in SPR1 showed association. (PMID:12930300)
  • SEEK1 polymorphisms +39604, +39709, and +26680 are not associated with Crohn’s disease in the Newfoundland population. (PMID:15301859)
  • Report PCR-RFLP genotyping assay for PSORS1C1 which is in linkage disequilibrium with HLA-B*58:01 and may be marker for allopurinol-related Stevens-Johnson syndrome/toxic epidermal necrolysis in Japanese. (PMID:22277675)
  • PSORS1C1 comparison showed association with the complete set of systemic sclerosis patients and all the subsets except for the anti-centromere-positive patients but, the association was dependent on different HLA class II alleles. (PMID:22896740)
  • this study demonstrates that SNPs in the PSORS1C1-encoding gene have a strong association with RA. (PMID:23769905)
  • PSORS1C1/CDSN gene may play a pathogenic role in ankylosing spondylitis (PMID:24210685)
  • The association has been found between PSORS1C1 SNPs and asthma in Hispanic Americans. (PMID:24406073)
  • ACPA were associated significantly with rs7574865 in STAT-4. The SNP rs2233945 in the PSORS1C1 gene was protective regarding the presence of bone erosions, while rs2542151 in PTPN2 gene was associated with joint damage. (PMID:27342690)
  • Patients carrying PSORS1C1 variant allele rs2233945 did not reach low disease activity at 6 months in both the whole RA group and Etanercept treated patients. (PMID:28107378)
  • The results of this study confirms the minor allele PSORS1C1 is positively associated with allopurinol-induced drug hypersensitivity. (PMID:29193002)
  • results show, for the first time, the male-only associations of the PSORS1C3 gene with psoriasis risk and of the PSORS1C1/CDSN gene with severity of disease. However, the age dependent associations need to be validated in larger sample sizes as well as in other populations. (PMID:29589160)
  • Psoriasis Susceptibility 1 Candidate 1 (PSORS1C1) Polymorphism is Associated with Autoimmune Thyroid Disease in a Chinese Han Population. (PMID:34325607)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Psoriasis susceptibility 1 candidate gene 1 protein — Q9UIG5 (reviewed: Q9UIG5)

Alternative names: Protein SEEK1

All UniProt accessions (4): A0A0C4DGJ2, D2IYL0, Q2M3K9, Q9UIG5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in skin. Also found in heart, placenta, liver, skeletal muscle and pancreas.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UIG5-11yes
Q9UIG5-22

RefSeq proteins (1): NP_054787* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR028206SEEK1Family

Pfam: PF15357

UniProt features (11 total): sequence variant 7, chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UIG5-F155.100.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): PEDRIOLI_MIR31_TARGETS_DN, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ALK_DN.V1_DN, KRAS.300_UP.V1_DN, KRAS.50_UP.V1_DN, KRAS.600_UP.V1_DN, KRAS.600.LUNG.BREAST_UP.V1_DN, KRAS.LUNG_UP.V1_DN, BARX1_TARGET_GENES, CBX7_TARGET_GENES, HMG20B_TARGET_GENES, TEAD2_TARGET_GENES, TOP2B_TARGET_GENES, ZNF146_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

374 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PSORS1C1CDSNQ15517945
PSORS1C1HLA-CP04222772
PSORS1C1CCHCR1Q8TD31645
PSORS1C1PSORS1C2Q9UIG4620
PSORS1C1TCF19Q9Y242594
PSORS1C1MCCD1P59942495
PSORS1C1HLA-BP01889479
PSORS1C1KLHL8Q9P2G9472
PSORS1C1TSBP1Q5SRN2471
PSORS1C1OR10C1Q96KK4462
PSORS1C1POLR1HQ9P1U0453
PSORS1C1HLA-DQB1P01917450
PSORS1C1C6orf15Q6UXA7447
PSORS1C1SOD1P00441429
PSORS1C1KRT1P04264422

IntAct

1 interactions, top by confidence:

BioGRID (1): PSORS1C1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GTK4, A0JNL8, A2RUT3, A4D1N5, A4D250, B1ANY3, C0HMD7, F1MQW7, F2Z3F1, J3KSC0, O14603, O95411, P0C092, P0DMR3, P37200, P47939, P47940, P69615, Q0VFX4, Q14695, Q32KZ5, Q3C1V9, Q4G0G2, Q4R3X9, Q52M75, Q53S99, Q5SR53, Q5SWW7, Q5T6R2, Q5W5W9, Q66669, Q66HF0, Q6AWC8, Q6DGF6, Q6ZP68, Q6ZV80, Q6ZVU0, Q7L4S7, Q7Z4H9, Q8N2C9

Diamond homologs: Q7YR46, Q9UIG5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

52 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance31
Likely benign4
Benign10

Top pathogenic / likely-pathogenic (0)

SpliceAI

1186 predictions. Top by Δscore:

VariantEffectΔscore
6:31114890:AGGTG:Adonor_loss1.0000
6:31117527:TCCCT:Tacceptor_loss1.0000
6:31117529:CCTG:Cacceptor_loss1.0000
6:31117530:C:CCacceptor_gain1.0000
6:31117530:CTGT:Cacceptor_loss1.0000
6:31133641:GCTAT:Gdonor_gain1.0000
6:31138302:GATGC:Gacceptor_gain1.0000
6:31138304:TGC:Tacceptor_gain1.0000
6:31138305:GC:Gacceptor_gain1.0000
6:31138306:CC:Cacceptor_gain1.0000
6:31138307:C:CAacceptor_loss1.0000
6:31138307:C:CCacceptor_gain1.0000
6:31114888:GAAG:Gdonor_gain0.9900
6:31114893:T:Gdonor_loss0.9900
6:31117525:GGTCC:Gacceptor_gain0.9900
6:31117526:GTCC:Gacceptor_gain0.9900
6:31117527:TCC:Tacceptor_gain0.9900
6:31117528:CC:Cacceptor_gain0.9900
6:31117528:CCC:Cacceptor_gain0.9900
6:31117529:CC:Cacceptor_gain0.9900
6:31117531:T:Cacceptor_loss0.9900
6:31133676:GAAA:Gdonor_gain0.9900
6:31138303:ATGC:Aacceptor_gain0.9900
6:31138309:G:Cacceptor_gain0.9900
6:31138309:G:GCacceptor_gain0.9900
6:31114892:G:GGdonor_gain0.9800
6:31129547:A:AGacceptor_gain0.9800
6:31129552:C:Gacceptor_gain0.9800
6:31133677:A:Tdonor_gain0.9800
6:31137566:AT:Aacceptor_gain0.9800

AlphaMissense

983 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:31139678:T:CF69L0.949
6:31139680:C:AF69L0.949
6:31139680:C:GF69L0.949
6:31138775:T:CF55L0.891
6:31138777:C:AF55L0.891
6:31138777:C:GF55L0.891
6:31139762:T:CF97L0.863
6:31139764:T:AF97L0.863
6:31139764:T:GF97L0.863
6:31139909:T:CF146L0.841
6:31139911:T:AF146L0.841
6:31139911:T:GF146L0.841
6:31139918:A:CS149R0.784
6:31139920:C:AS149R0.784
6:31139920:C:GS149R0.784
6:31139679:T:CF69S0.708
6:31139729:G:CD86H0.695
6:31139841:T:CI123T0.690
6:31139641:G:CW56C0.667
6:31139641:G:TW56C0.667
6:31139739:T:AV89D0.659
6:31139733:T:CI87T0.652
6:31139648:G:TG59W0.651
6:31139733:T:GI87S0.630
6:31139730:A:TD86V0.610
6:31139719:G:CR82S0.605
6:31139719:G:TR82S0.605
6:31139679:T:GF69C0.601
6:31139841:T:GI123S0.600
6:31139710:A:CR79S0.590

dbSNP variants (sampled 300 via entrez): RS1000289720 (6:31139431 C>T), RS1000602109 (6:31121823 G>A,C), RS1000647534 (6:31133424 C>T), RS1000655376 (6:31127577 A>G), RS1000707506 (6:31127234 A>G), RS1000861584 (6:31127389 C>T), RS1000949975 (6:31122052 A>G), RS1001009016 (6:31133286 G>A), RS1001140627 (6:31122145 C>A), RS1001162849 (6:31118426 G>C), RS1001275337 (6:31124209 C>T), RS1001340329 (6:31130463 G>A), RS1001774408 (6:31128007 A>G), RS1001920328 (6:31121381 G>A), RS1002033998 (6:31113456 A>C,G)

Disease associations

OMIM: gene MIM:613525 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

94 associations (top):

StudyTraitp-value
GCST000589_3White blood cell count7.000000e-09
GCST000984_14Idiopathic membranous nephropathy1.000000e-42
GCST001137_9White blood cell count4.000000e-13
GCST001146_4Systemic sclerosis6.000000e-10
GCST001181_2Drug-induced Stevens-Johnson syndrome or toxic epidermal necrolysis (SJS/TEN)3.000000e-07
GCST001239_1Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS-TEN)2.000000e-08
GCST001729_10Crohn’s disease5.000000e-28
GCST001737_11Chronic obstructive pulmonary disease-related biomarkers6.000000e-09
GCST001737_12Chronic obstructive pulmonary disease-related biomarkers8.000000e-09
GCST001768_5Behcet’s disease2.000000e-20
GCST001779_4Hematology traits5.000000e-07
GCST001812_2Epstein-Barr virus immune response (EBNA-1)2.000000e-10
GCST002140_3Multiple myeloma1.000000e-10
GCST002647_135Height2.000000e-32
GCST002702_21Height2.000000e-07
GCST002876_3Type 1 diabetes and autoimmune thyroid diseases1.000000e-22
GCST002884_7Cutaneous lupus erythematosus4.000000e-10
GCST003542_141Night sleep phenotypes5.000000e-06
GCST003833_1Adult asthma2.000000e-11
GCST003833_17Adult asthma7.000000e-08
GCST004131_25Inflammatory bowel disease2.000000e-31
GCST004133_79Ulcerative colitis5.000000e-65
GCST004521_103Autism spectrum disorder or schizophrenia2.000000e-08
GCST004521_114Autism spectrum disorder or schizophrenia3.000000e-17
GCST004521_117Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_126Autism spectrum disorder or schizophrenia2.000000e-10
GCST004521_132Autism spectrum disorder or schizophrenia2.000000e-09
GCST004521_16Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_19Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_2Autism spectrum disorder or schizophrenia2.000000e-16

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0005081surfactant protein D measurement
EFO:0004645response to vaccine
EFO:0009180rosacea severity measurement
EFO:0005298allergic sensitization measurement
EFO:0009598feeling miserable measurement
EFO:0009597feeling nervous measurement
EFO:0004761uric acid measurement
EFO:0004615apolipoprotein B measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

5 annotations.

VariantTypeLevelDrugsPhenotypes
rs2233945Efficacy3etanerceptRheumatoid arthritis
rs3130985Toxicity3carboplatin;gemcitabineNon-Small Cell Lung Carcinoma;Thrombocytopenia
rs3131003Toxicity3allopurinolSevere Cutaneous Adverse Reactions
rs3815087Toxicity4allopurinolSevere Cutaneous Adverse Reactions;Stevens-Johnson Syndrome;Toxic Epidermal Necrolysis
rs9263726Toxicity3allopurinolDrug Reaction with Eosinophilia and Systemic Symptoms;Stevens-Johnson Syndrome

PharmGKB variants

5 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2233945PSORS1C1, PSORS1C232.501etanercept
rs3815087PSORS1C14-2.501allopurinol
rs9263726PSORS1C1, PSORS1C233.751allopurinol
rs3131003PSORS1C133.001allopurinol
rs3130985CDSN, PSORS1C132.501carboplatin;gemcitabine

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Silicon Dioxidedecreases expression, increases expression2
bisphenol Adecreases methylation1
CGP 52608affects binding, increases reaction1
Resveratrolaffects cotreatment, decreases expression1
Arsenicaffects methylation1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Estradiolaffects expression1
Oxygenincreases expression1
Phthalic Acidsincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Testosteronedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutiondecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 73

This page pulls from 73 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot