CYYR1

gene
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Summary

CYYR1 (cysteine and tyrosine rich 1, HGNC:16274) is a protein-coding gene on chromosome 21q21.3, encoding Cysteine and tyrosine-rich protein 1 (Q96J86).

Predicted to be located in membrane.

Source: NCBI Gene 116159 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 38 total — 1 pathogenic
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_001320768

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16274
Approved symbolCYYR1
Namecysteine and tyrosine rich 1
Location21q21.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000166265
Ensembl biotypeprotein_coding
OMIM616020
Entrez116159

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000299340, ENST00000400043, ENST00000652641

RefSeq mRNA: 2 — MANE Select: NM_001320768 NM_001320768, NM_052954

CCDS: CCDS13578, CCDS93083

Canonical transcript exons

ENST00000652641 — 4 exons

ExonStartEnd
ENSE000011015462656626626566368
ENSE000036945692648027226480429
ENSE000038463942657286826573286
ENSE000038474102646621626468634

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 97.58.

FANTOM5 (CAGE): breadth broad, TPM avg 7.5428 / max 179.7619, expressed in 680 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1900103.5159625
1900091.4844437
1900071.1451387
1900080.9200329
1900060.2619158
1900050.2155143

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
visceral pleuraUBERON:000240197.58gold quality
left ventricle myocardiumUBERON:000656696.30gold quality
parietal pleuraUBERON:000240095.93gold quality
pericardiumUBERON:000240795.66gold quality
vena cavaUBERON:000408795.36gold quality
mammary ductUBERON:000176594.33gold quality
epithelium of mammary glandUBERON:000324494.33gold quality
heart right ventricleUBERON:000208094.15gold quality
urethraUBERON:000005794.00gold quality
myocardiumUBERON:000234993.87gold quality
superficial temporal arteryUBERON:000161493.59gold quality
cardia of stomachUBERON:000116293.53gold quality
mammary glandUBERON:000191193.47gold quality
thoracic mammary glandUBERON:000520093.43gold quality
lower lobe of lungUBERON:000894993.16gold quality
adrenal cortexUBERON:000123592.84gold quality
epithelial cell of pancreasCL:000008392.74gold quality
adrenal tissueUBERON:001830392.48gold quality
right adrenal gland cortexUBERON:003582792.48gold quality
left adrenal gland cortexUBERON:003582592.47gold quality
adrenal glandUBERON:000236992.32gold quality
right adrenal glandUBERON:000123392.18gold quality
left adrenal glandUBERON:000123492.18gold quality
tibiaUBERON:000097991.96gold quality
subcutaneous adipose tissueUBERON:000219091.67gold quality
layer of synovial tissueUBERON:000761691.59gold quality
cardiac muscle of right atriumUBERON:000337991.32silver quality
omental fat padUBERON:001041491.24gold quality
peritoneumUBERON:000235891.23gold quality
adipose tissue of abdominal regionUBERON:000780891.05gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-MTAB-6678yes1117.41
E-MTAB-10287yes75.31
E-GEOD-134144yes47.66
E-HCAD-11yes46.13
E-GEOD-135922yes40.56
E-MTAB-6701yes29.90
E-HCAD-1yes29.24
E-CURD-46yes25.65
E-MTAB-5061yes20.06
E-GEOD-83139yes9.83
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting CYYR1, 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-5692A100.0074.406850
HSA-MIR-4673100.0066.641490
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-186-5P99.9970.833707
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-548P99.9872.253784
HSA-MIR-9-3P99.9670.882068
HSA-MIR-570-3P99.9672.414910
HSA-MIR-211099.9666.681930
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-545-3P99.9570.742783
HSA-MIR-96-5P99.9572.802140
HSA-MIR-1213399.9271.822006
HSA-MIR-205-3P99.9269.923165
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-137-3P99.8774.742401
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-629-3P99.8567.991875
HSA-MIR-576-5P99.8470.462582
HSA-MIR-132399.8369.892471
HSA-MIR-442099.8270.081624
HSA-MIR-3180-5P99.8269.122422

Literature-anchored findings (GeneRIF, showing 3)

  • A new “subtle” splicing isoform (CAG+) of CYYR1 mRNA, the sequence & expression of this gene were defined in a series of NE tumors. This CAG+ codon determines the presence of an Ala residue at the exon 3/exon 4 junction of the CYYR1 mRNA. (PMID:17442112)
  • New CYYR1 alternative isoforms were identified and characterized. (PMID:24981926)
  • CYYR1 promotes the degradation of the E3 ubiquitin ligase WWP1 and is associated with favorable prognosis in breast cancer. (PMID:39059493)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCyyr1ENSMUSG00000041134
rattus_norvegicusCyyr1ENSRNOG00000001544

Protein

Protein identifiers

Cysteine and tyrosine-rich protein 1Q96J86 (reviewed: Q96J86)

Alternative names: Proline-rich domain-containing protein

All UniProt accessions (1): Q96J86

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Widely expressed.

Similarity. Belongs to the CYYR1 family.

Isoforms (6)

UniProt IDNamesCanonical?
Q96J86-11yes
Q96J86-22
Q96J86-33
Q96J86-44
Q96J86-55
Q96J86-66

RefSeq proteins (2): NP_001307697, NP_443186 (=MANE)

Domains & families (InterPro)

IDNameType
IPR022640CYYR1Family

Pfam: PF10873

UniProt features (18 total): splice variant 9, sequence variant 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96J86-F159.390.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): MODULE_255, MODULE_317, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, RIGGI_EWING_SARCOMA_PROGENITOR_UP, TAATTA_CHX10_01, MODULE_69, HATADA_METHYLATED_IN_LUNG_CANCER_UP, chr21q21, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MODULE_37, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_2H_DN, MIR570_3P

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure1

Protein interactions and networks

STRING

698 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYYR1SLC4A11Q8NBS3647
CYYR1COL8A2P25067572
CYYR1SHISAL1Q3SXP7503
CYYR1MRPL39Q9NYK5493
CYYR1VOPP1Q96AW1445
CYYR1WBP1Q96G27434
CYYR1SLC16A14Q7RTX9428
CYYR1CTXND1A0A1B0GTU2419
CYYR1CCDC177Q9NQR7408
CYYR1GAGE12JA6NER3372
CYYR1GPC4O75487365
CYYR1C2CD2Q9Y426363
CYYR1SPRED3Q2MJR0358
CYYR1CLDN14O95500349
CYYR1GAGE12BA1L429348
CYYR1GIMAP6Q6P9H5348

IntAct

4 interactions, top by confidence:

ABTypeScore
CYYR1YAP1psi-mi:“MI:0914”(association)0.350
CYYR1PTPRFpsi-mi:“MI:0914”(association)0.350
feoACYYR1psi-mi:“MI:0915”(physical association)0.000

BioGRID (12): GOPC (Affinity Capture-MS), MAGI1 (Affinity Capture-MS), YAP1 (Affinity Capture-MS), MAGI1 (Affinity Capture-MS), YAP1 (Affinity Capture-MS), YAP1 (Affinity Capture-MS), MAGI1 (Affinity Capture-MS), PTPRF (Affinity Capture-MS), NEDD4 (Affinity Capture-MS), GOPC (Affinity Capture-MS), WWOX (Affinity Capture-MS), NEDD4L (Affinity Capture-MS)

ESM2 similar proteins: A0PJX4, A2A8U2, A4D2P6, A6QM06, D4A6L0, E1BBQ2, O15079, O60320, P12755, P49797, P97260, Q0D2I5, Q12770, Q15884, Q1RMB5, Q3TS39, Q3UPR0, Q4FZH1, Q5MNU5, Q5SNT2, Q5T848, Q5XKK7, Q60698, Q6A044, Q7T0Z7, Q7TMB0, Q7TPB0, Q810F0, Q86XR5, Q8BX43, Q8BXL9, Q8C419, Q8CA71, Q8K064, Q8K2Y3, Q8N114, Q8NDY8, Q8WV15, Q91WM6, Q92537

Diamond homologs: Q5HZN7, Q5PQS5, Q6NYG4, Q8VIH7, Q96J86

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance33
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
127268NC_000021.7:g.13636378_28138533dupPathogenic

SpliceAI

1331 predictions. Top by Δscore:

VariantEffectΔscore
21:26480427:CCC:Cacceptor_gain1.0000
21:26480428:CC:Cacceptor_gain1.0000
21:26480428:CCC:Cacceptor_gain1.0000
21:26480428:CCCTA:Cacceptor_loss1.0000
21:26480429:CC:Cacceptor_gain1.0000
21:26480430:C:CCacceptor_gain1.0000
21:26480430:CTA:Cacceptor_loss1.0000
21:26480431:T:Cacceptor_loss1.0000
21:26565505:AAC:Adonor_gain1.0000
21:26566257:AATAC:Adonor_loss1.0000
21:26566258:ATACT:Adonor_loss1.0000
21:26566259:TAC:Tdonor_loss1.0000
21:26566260:ACTC:Adonor_loss1.0000
21:26566261:CT:Cdonor_loss1.0000
21:26566262:TCACG:Tdonor_loss1.0000
21:26566263:C:CGdonor_loss1.0000
21:26566264:A:ACdonor_gain1.0000
21:26566264:ACG:Adonor_loss1.0000
21:26566265:C:Adonor_loss1.0000
21:26566265:C:CAdonor_gain1.0000
21:26566265:CG:Cdonor_gain1.0000
21:26566265:CGAG:Cdonor_gain1.0000
21:26566364:ATCAT:Aacceptor_gain1.0000
21:26566365:TCAT:Tacceptor_gain1.0000
21:26566366:CAT:Cacceptor_gain1.0000
21:26566366:CATC:Cacceptor_gain1.0000
21:26566367:ATC:Aacceptor_loss1.0000
21:26566368:TC:Tacceptor_loss1.0000
21:26566369:C:CCacceptor_gain1.0000
21:26566369:C:CGacceptor_loss1.0000

AlphaMissense

1002 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:26480383:C:GG75R0.997
21:26480383:C:TG75R0.997
21:26480400:C:TG69E0.997
21:26480401:C:GG69R0.996
21:26480401:C:TG69R0.996
21:26480412:C:TG65D0.996
21:26480413:C:GG65R0.995
21:26480371:C:GG79R0.994
21:26480371:C:TG79R0.994
21:26480373:G:TA78D0.994
21:26480359:A:GC83R0.993
21:26480361:A:TI82K0.993
21:26480370:C:TG79E0.993
21:26480402:A:CF68L0.993
21:26480402:A:TF68L0.993
21:26480404:A:GF68L0.993
21:26480382:C:TG75E0.992
21:26480394:A:TV71E0.992
21:26480397:A:TI70K0.992
21:26566299:C:TC48Y0.992
21:26480418:A:TI63N0.991
21:26566298:G:CC48W0.991
21:26566300:A:GC48R0.991
21:26566301:A:CC47W0.991
21:26480385:A:TM74K0.990
21:26480406:A:TV67D0.990
21:26480415:G:TA64E0.990
21:26566299:C:GC48S0.990
21:26566300:A:TC48S0.990
21:26566325:G:CC39W0.990

dbSNP variants (sampled 300 via entrez): RS1000085472 (21:26467428 A>T), RS1000108020 (21:26551709 G>A,T), RS1000124863 (21:26506077 A>G), RS1000139607 (21:26466961 T>C), RS1000149669 (21:26508316 C>G), RS1000163224 (21:26488350 G>C), RS1000218364 (21:26559023 C>T), RS1000242027 (21:26497105 A>C), RS1000251408 (21:26525989 G>A), RS1000253707 (21:26483462 A>T), RS1000313603 (21:26473052 C>G), RS1000323987 (21:26519602 A>C,G), RS1000353079 (21:26545236 T>C), RS1000360421 (21:26565912 C>A,G), RS1000371425 (21:26480032 C>A,G)

Disease associations

OMIM: gene MIM:616020 | disease phenotypes: MIM:605714

GenCC curated gene-disease

Mondo (2): Alzheimer disease (MONDO:0004975), cerebral amyloid angiopathy, APP-related (MONDO:0011583)

Orphanet (9): ABeta amyloidosis, Dutch type (Orphanet:100006), Early-onset autosomal dominant Alzheimer disease (Orphanet:1020), ABetaL34V amyloidosis (Orphanet:324703), ABeta amyloidosis, Iowa type (Orphanet:324708), ABeta amyloidosis, Italian type (Orphanet:324713), ABetaA21G amyloidosis (Orphanet:324718), ABeta amyloidosis, Arctic type (Orphanet:324723), Hereditary cerebral amyloid angiopathy (Orphanet:85458), NON RARE IN EUROPE: Alzheimer disease (Orphanet:238616)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0002511Alzheimer disease

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001621_1Airflow obstruction4.000000e-06
GCST003207_5Response to exercise (triglyceride level interaction)2.000000e-06
GCST009996_9HDL cholesterol levels9.000000e-07

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0007681triglyceride change measurement
EFO:0007768response to exercise
EFO:0007805HDL cholesterol change measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D000544Alzheimer DiseaseC10.228.140.380.100; C10.574.945.249; F03.615.400.100

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression4
methylmercuric chlorideincreases expression, affects cotreatment3
Tobacco Smoke Pollutiondecreases expression2
sodium arsenatedecreases expression, increases abundance1
arsenitedecreases expression1
cobaltous chloridedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinincreases expression, affects cotreatment1
bisphenol Sincreases methylation1
Sunitinibdecreases expression1
Acetaminophenincreases expression1
Ethanoldecreases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Cadmiumdecreases expression1
Silicon Dioxideincreases expression1
Testosteronedecreases expression1
Aflatoxin B1decreases methylation1
Cadmium Chloridedecreases expression1
Permethrindecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00009191PHASE4COMPLETEDThe Depression in Alzheimer’s Disease Study (DIADS)
NCT00009217PHASE4COMPLETEDTreatment of Behavioral Symptoms in Alzheimer’s Disease
NCT00018278PHASE4COMPLETEDElectrophysiologic Measures of Treatment Response in Alzheimer Disease
NCT00035204PHASE4COMPLETEDA Study of the Effects on Sleep, Attention, and Gastrointestinal Tolerance of Galantamine and Donepezil in Patients With Alzheimer’s Disease
NCT00042172PHASE4COMPLETEDTreatment for Early Memory Loss
NCT00046358PHASE4COMPLETEDThe Effect of Short-Term Statins and NSAIDs on Levels of Beta-Amyloid, a Protein Associated With Alzheimer’s Disease
NCT00104442PHASE4COMPLETEDStudy of the Effects of Current Drug Treatments on Levels of Certain Brain Chemicals in Alzheimer’s Disease
NCT00120874PHASE4COMPLETEDMemantine and Comprehensive, Individualized Management of Alzheimer’s Disease and Caregiver Training
NCT00142324PHASE4UNKNOWNCALM-AD
NCT00165724PHASE4COMPLETEDAlzheimer’s Disease Long-term Follow-up Study (ALF Study)
NCT00165750PHASE4TERMINATEDCorrelation Between Regional Brain Volume and Response to Donepezil Treatment in AD Patients
NCT00202124PHASE4COMPLETEDDouble Blind Study of Trp01 in Patients With Alzheimer’s Disease
NCT00208819PHASE4COMPLETEDA Comparison of Two Standard Therapies in the Management of Dementia With Agitation
NCT00216515PHASE4COMPLETEDThe Efficacy of Galantamine on the Attention and the Frontal Function of the Patients With Dementia of Alzheimer Type
NCT00230568PHASE4COMPLETEDEARTH 413: A Study of Aricept in Hispanic Patients With Mild to Moderate Alzheimer’s Disease (AD)
NCT00234637PHASE4COMPLETEDRivastigmine Monotherapy and Combination Therapy With Memantine in Patients With Moderately Severe Alzheimer’s Disease Who Failed to Benefit From Previous Cholinesterase Inhibitor Treatment
NCT00245206PHASE4COMPLETEDSide Effects of Newer Antipsychotics in Older Adults
NCT00254033PHASE4COMPLETEDApathy Associated With Alzheimer’s Disease
NCT00260624PHASE4COMPLETEDEscitalopram Treatment of Patients With Agitated Dementia
NCT00303277PHASE4COMPLETEDDo HMG CoA Reductase Inhibitors Affect Abeta Levels?
NCT00305903PHASE4COMPLETEDSafety and Tolerability of Rivastigmine With Add-on Memantine in Patients With Probable Alzheimer’s Disease
NCT00306124PHASE4UNKNOWNDopaminergic Enhancement of Learning and Memory in Healthy Adults and Patients With Dementia/Mild Cognitive Impairment
NCT00334906PHASE4COMPLETEDStudy of Memantine in Assessment of Selected Measures of Volumetric Magnetic Resonance Imaging (MRI) and Cognition in Moderate AD (Alzheimer’s Disease)
NCT00369603PHASE4TERMINATEDFunctional Brain Imaging of Medication Treatment Response in Mild Alzheimer’s Disease Patients
NCT00375557PHASE4WITHDRAWNSafety and Efficacy of Divalproex and Quetiapine in Elderly Alzheimer’s Dementia Patients
NCT00381381PHASE4COMPLETEDThe Clinical Response of Choline Acetyltransferase and Apolipoprotein Epsilon Gene Polymorphisms to Donepezil in Alzheimer’s Disease
NCT00385684PHASE4COMPLETEDLow-Dose Opiate Therapy for Discomfort in Dementia (L-DOT)
NCT00401167PHASE4COMPLETEDMemantine for Agitation and Aggression in Severe Alzheimer’s Disease
NCT00403520PHASE4COMPLETEDHippocampus Study: Comparative Effect of Donepezil 10mg/d and Placebo on Clinical and Radiological Markers
NCT00417482PHASE4COMPLETEDAntipsychotic Discontinuation in Alzheimer’s Disease
NCT00443014PHASE4COMPLETEDThe Dementia Study in Northern Norway
NCT00469456PHASE4COMPLETEDEffect of Memantine on Functional Communication in Patients With Alzheimer’s Disease
NCT00476008PHASE4COMPLETEDDelaying the Progression of Driving Impairment in Individuals With Mild Alzheimer’s Disease
NCT00477659PHASE4COMPLETEDNeural Correlates In Mild Alzheimer’s Disease
NCT00480870PHASE4COMPLETEDThe Effect of Anticholinesterase Drugs on Sleep in Alzheimer’s Disease Patients
NCT00495820PHASE4COMPLETEDMethylphenidate for Apathy in Alzheimer’s Dementia: A Controlled Study
NCT00523666PHASE4UNKNOWNDiffusion Tensor Weighted MRI in Alzheimer’s Disease Modifying Treatment Effects of Galantamine (Reminyl®)
NCT00549601PHASE4COMPLETEDConvenience, Tolerability, and Safety of Change in the Administration of Rivastigmine From Capsules to a Transdermal Patch in Patients With Mild to Moderate Alzheimer’s Disease
NCT00551161PHASE4COMPLETEDMagnetic Resonance Spectroscopy Study of Memantine in Alzheimer’s Disease
NCT00561392PHASE4COMPLETEDClinical Effectiveness of 10 cm^2 Rivastigmine Patch in Patients With Alzheimer’s Disease
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cerebral amyloid angiopathy, APP-related