SCARA3

gene
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Also known as CSR1CSRMSLR1APC7MSRL1

Summary

SCARA3 (scavenger receptor class A member 3, HGNC:19000) is a protein-coding gene on chromosome 8p21.1, encoding Scavenger receptor class A member 3 (Q6AZY7). Seems to protect cells by scavenging oxidative molecules or harmful products of oxidation.

This gene encodes a macrophage scavenger receptor-like protein. This protein has been shown to deplete reactive oxygen species, and thus play an important role in protecting cells from oxidative stress. The expression of this gene is induced by oxidative stress. Alternatively spliced transcript variants encoding distinct isoforms have been described.

Source: NCBI Gene 51435 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 109 total
  • MANE Select transcript: NM_016240

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19000
Approved symbolSCARA3
Namescavenger receptor class A member 3
Location8p21.1
Locus typegene with protein product
StatusApproved
AliasesCSR1, CSR, MSLR1, APC7, MSRL1
Ensembl geneENSG00000168077
Ensembl biotypeprotein_coding
OMIM602728
Entrez51435

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000301904, ENST00000337221, ENST00000890601, ENST00000890602, ENST00000890603, ENST00000890604, ENST00000890605, ENST00000890606, ENST00000890607, ENST00000890608, ENST00000932941, ENST00000970378

RefSeq mRNA: 2 — MANE Select: NM_016240 NM_016240, NM_182826

CCDS: CCDS34870, CCDS34871

Canonical transcript exons

ENST00000301904 — 6 exons

ExonStartEnd
ENSE000011201362764970227649800
ENSE000011201382765150827651627
ENSE000011201392765678227656880
ENSE000011201402765849627659539
ENSE000011201412767090027673018
ENSE000012919872763390227634207

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 97.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6130 / max 166.9200, expressed in 1276 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
881677.48741255
881660.4003236
881680.3572178
881690.209598
881650.153578
2051380.00521

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370197.74gold quality
right uterine tubeUBERON:000130296.55gold quality
right coronary arteryUBERON:000162596.04gold quality
body of uterusUBERON:000985395.64gold quality
thoracic aortaUBERON:000151595.61gold quality
ascending aortaUBERON:000149695.58gold quality
descending thoracic aortaUBERON:000234595.54gold quality
left uterine tubeUBERON:000130394.87gold quality
tendonUBERON:000004394.41gold quality
tendon of biceps brachiiUBERON:000818894.03gold quality
aortaUBERON:000094793.53gold quality
endocervixUBERON:000045893.33gold quality
putamenUBERON:000187492.32gold quality
popliteal arteryUBERON:000225092.04gold quality
tibial arteryUBERON:000761092.02gold quality
left lobe of thyroid glandUBERON:000112092.00gold quality
smooth muscle tissueUBERON:000113591.87gold quality
gall bladderUBERON:000211091.67gold quality
ventricular zoneUBERON:000305391.63gold quality
layer of synovial tissueUBERON:000761691.63gold quality
caudate nucleusUBERON:000187391.56gold quality
myometriumUBERON:000129691.51gold quality
right lobe of thyroid glandUBERON:000111991.38gold quality
mucosa of stomachUBERON:000119991.23gold quality
lower esophagus muscularis layerUBERON:003583391.18gold quality
lower esophagusUBERON:001347391.16gold quality
seminal vesicleUBERON:000099891.11gold quality
sural nerveUBERON:001548891.09gold quality
synovial jointUBERON:000221790.93gold quality
thyroid glandUBERON:000204690.79gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-114yes25.92
E-ANND-3yes6.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting SCARA3, 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-6867-5P100.0082.213464
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-511-3P99.9968.851467
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-202-5P99.7867.65991
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-453099.6966.471509
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-64699.6867.841645
HSA-MIR-6762-3P99.6666.941188
HSA-MIR-4666B99.6468.691282
HSA-MIR-56799.6368.571219
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-391599.4568.491905
HSA-MIR-29799.4069.581418
HSA-MIR-431699.3765.751360
HSA-MIR-542-3P99.3467.581270
HSA-MIR-183-5P99.3172.271164
HSA-MIR-5589-3P99.2968.301443
HSA-MIR-223-5P99.2468.821206
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-6809-5P99.1368.451223
HSA-MIR-92299.0267.231838
HSA-MIR-427099.0266.261987
HSA-MIR-143-5P98.9868.87946
HSA-MIR-3190-5P98.8764.891345
HSA-MIR-770598.6967.47543

Literature-anchored findings (GeneRIF, showing 15)

  • Down-regulation of CSR1 protein expression by promoter methylation is associated with tumor growth and metastasis of prostate cancer (PMID:16436673)
  • CSR1 appears to induce cell death through a novel mechanism by hijacking a critical RNA processing enzyme CPSF3. (PMID:18806823)
  • The consistently high SCARA3 levels in both primary carcinomas and metastatic cells in effusions, and its up-regulation along disease progression from diagnosis to recurrence, suggest a role in ovarian cancer biology. (PMID:21855113)
  • Results demonstrate the involvement of SCARA3 and SCARA5 in the uptake of PF14-oligonucleotide nanocomplexes. (PMID:22138034)
  • The binding of CSR1 with XIAP enhanced caspase-9 and caspase-3 protease activities. (PMID:22683311)
  • Data indicate that the clinical samples showed an inverse correlation between SCARA3 gene expression, myeloma progression, and favorable clinical prognosis. (PMID:23537707)
  • Findings regarding the interaction of NADPH-P450 reductase (NPR) with cellular stress response (CSR) indicated function of NPR in hypoxic response. (PMID:24491563)
  • Suppression of CSR1 expression is a novel mechanism critical for the oncogenic activity of miR-650. (PMID:25956032)
  • The interaction between CSR1 and SF3A3 led to migration of SF3A3 from nucleus to cytoplasm. The cytoplasmic redistribution of SF3A3 significantly reduced the splicing efficiency of epidermal growth factor receptor and platelet-derived growth factor receptor. (PMID:27148859)
  • demonstrated that CSR1 inhibited hepatocellular carcinoma cell proliferation, migration and invasion through inactivation of hematopoietic PBX interacting protein (HPIP) and its downstream PI3K/AKT signaling pathway. (PMID:28975986)
  • CSR1 is SUMOylated at K582 and rapid ubiquitinated and degradated in prostate cancer cells. (PMID:29705808)
  • Study found that SCARA3 is associated with severity of hand, foot, and mouth disease, and it may be a potential prognostic marker to predict the HFMD progression in EV71 infected patients. (PMID:31577778)
  • Identification of SCARA3 with potential roles in metabolic disorders. (PMID:33318306)
  • DICER-AS1 functions as competing endogenous RNA that targets CSR1 by sponging microRNA-650 and suppresses gastric cancer progression. (PMID:34586953)
  • SCARA3 inhibits cell proliferation and EMT through AKT signaling pathway in lung cancer. (PMID:35578316)

Cross-species orthologs

15 orthologs

OrganismSymbolGene ID
danio_rerioscara3ENSDARG00000008060
mus_musculusScara3ENSMUSG00000034463
rattus_norvegicusScara3ENSRNOG00000016177
caenorhabditis_elegansWBGENE00000599
caenorhabditis_eleganscol-35WBGENE00000612
caenorhabditis_eleganscol-47WBGENE00000624
caenorhabditis_eleganscol-50WBGENE00000627
caenorhabditis_elegansWBGENE00000661
caenorhabditis_elegansWBGENE00000700
caenorhabditis_elegansWBGENE00000701
caenorhabditis_elegansWBGENE00000717
caenorhabditis_elegansWBGENE00000718
caenorhabditis_elegansWBGENE00000721
caenorhabditis_elegansWBGENE00000757
caenorhabditis_elegansWBGENE00000760

Paralogs (2): METTL24 (ENSG00000053328), CTHRC1 (ENSG00000164932)

Protein

Protein identifiers

Scavenger receptor class A member 3Q6AZY7 (reviewed: Q6AZY7)

Alternative names: Cellular stress response gene protein

All UniProt accessions (1): Q6AZY7

UniProt curated annotations — full annotation on UniProt →

Function. Seems to protect cells by scavenging oxidative molecules or harmful products of oxidation.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus membrane.

Tissue specificity. Expressed ubiquitously.

Isoforms (2)

UniProt IDNamesCanonical?
Q6AZY7-11, CSR1yes
Q6AZY7-22, CSR2

RefSeq proteins (2): NP_057324, NP_878185 (=MANE)

Domains & families (InterPro)

IDNameType
IPR008160CollagenRepeat
IPR052376Oxidative_Scav/GlycosyltransFamily

Pfam: PF01391

UniProt features (30 total): glycosylation site 10, sequence variant 6, compositionally biased region 4, topological domain 2, splice variant 2, domain 2, chain 1, transmembrane region 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6AZY7-F170.760.36

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (10): 115, 182, 224, 257, 313, 337, 365, 400, 430, 451

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 127 (showing top): MODULE_255, GOCC_COLLAGEN_TRIMER, MODULE_317, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_UV_PROTECTION, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, chr8p21, MARTINEZ_RB1_TARGETS_DN, RIGGI_EWING_SARCOMA_PROGENITOR_DN, GOBP_RESPONSE_TO_UV, GOBP_RESPONSE_TO_RADIATION, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_RESPONSE_TO_LIGHT_STIMULUS

GO Biological Process (3): response to oxidative stress (GO:0006979), UV protection (GO:0009650), vesicle-mediated transport (GO:0016192)

GO Molecular Function (2): scavenger receptor activity (GO:0005044), protein binding (GO:0005515)

GO Cellular Component (6): Golgi membrane (GO:0000139), collagen trimer (GO:0005581), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
response to stress1
response to UV1
transport1
cellular process1
cargo receptor activity1
binding1
Golgi apparatus1
bounding membrane of organelle1
protein-containing complex1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

1496 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCARA3CPSF3Q9UKF6966
SCARA3CPSF2Q9P2I0751
SCARA3DCLRE1AQ6PJP8549
SCARA3FBF1Q8TES7546
SCARA3BLOC1S1P78537504
SCARA3PIWIL1Q96J94480
SCARA3ALG3Q92685480
SCARA3PIWIL4Q7Z3Z4479
SCARA3IER3P46695464
SCARA3HGSNATQ68CP4452
SCARA3FREM1Q5H8C1445
SCARA3PDCD11Q14690439
SCARA3SRCP12931436
SCARA3IRS1P35568434
SCARA3BPIFB2Q8N4F0429

IntAct

47 interactions, top by confidence:

ABTypeScore
MMP9TIMP1psi-mi:“MI:0914”(association)0.640
B3GAT3GOLIM4psi-mi:“MI:0914”(association)0.640
COLEC12SCARA3psi-mi:“MI:0915”(physical association)0.620
SCARA3SYNGR2psi-mi:“MI:0915”(physical association)0.560
SYNGR2SCARA3psi-mi:“MI:0915”(physical association)0.560
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
LGALS3PODXLpsi-mi:“MI:0914”(association)0.530
PLOD3PLOD2psi-mi:“MI:0914”(association)0.530
ABHD14ATMEM259psi-mi:“MI:0914”(association)0.530
LAIR2LAMA5psi-mi:“MI:0914”(association)0.530
LGALS1PODXLpsi-mi:“MI:0914”(association)0.530
SDC1ILVBLpsi-mi:“MI:0915”(physical association)0.400
CNOT7SCARA3psi-mi:“MI:0915”(physical association)0.370
SCARA3DEGS1psi-mi:“MI:0914”(association)0.350
LAIR2PLOD3psi-mi:“MI:0914”(association)0.350
TMEM106ATMEM131Lpsi-mi:“MI:0914”(association)0.350
BRICD5TMEM131Lpsi-mi:“MI:0914”(association)0.350
IL5RAPOTEFpsi-mi:“MI:0914”(association)0.350
TMEM87APOTEFpsi-mi:“MI:0914”(association)0.350
NCR3POTEFpsi-mi:“MI:0914”(association)0.350
DNAJB9POTEFpsi-mi:“MI:0914”(association)0.350
SCN3BA2ML1psi-mi:“MI:0914”(association)0.350
MFAP4QSOX1psi-mi:“MI:0914”(association)0.350
PRG2QSOX1psi-mi:“MI:0914”(association)0.350
C1QTNF9BRTCApsi-mi:“MI:0914”(association)0.350
PLOD1PLOD2psi-mi:“MI:0914”(association)0.350
C1QTNF1PLOD2psi-mi:“MI:0914”(association)0.350

BioGRID (152): SCARA3 (Two-hybrid), SCARA3 (Affinity Capture-RNA), SCARA3 (Affinity Capture-RNA), SCARA3 (Affinity Capture-RNA), SCARA3 (Affinity Capture-MS), COLEC12 (Affinity Capture-MS), XPO7 (Affinity Capture-MS), COCH (Affinity Capture-MS), HLA-A (Affinity Capture-MS), PXDN (Affinity Capture-MS), ABHD14A (Affinity Capture-MS), ATR (Affinity Capture-MS), HEATR3 (Affinity Capture-MS), SENP1 (Affinity Capture-MS), IQCB1 (Affinity Capture-MS)

ESM2 similar proteins: A2VE00, A2VE53, A2XW69, A5PMY6, A6QP79, B2RPV6, F1QC17, F7DP49, O75071, Q07065, Q0II90, Q13201, Q2LK54, Q32L59, Q3UIJ9, Q4V7C8, Q4V885, Q53EZ4, Q5BIX7, Q5EAJ6, Q5EB94, Q5KU26, Q5R6R3, Q5R923, Q5RI56, Q5ZM60, Q61595, Q640L3, Q6AZY7, Q6NRC9, Q6P6L0, Q70UQ0, Q7XU27, Q7Z7B0, Q84VY2, Q8BGQ6, Q8BIS8, Q8BMK4, Q8BT07, Q8BVC4

Diamond homologs: Q6AZY7, Q8C850

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 59 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Post-translational protein phosphorylation512.8×1e-03
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)511.1×2e-03
Extracellular matrix organization69.7×1e-03
Neutrophil degranulation84.7×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance91
Likely benign11
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

859 predictions. Top by Δscore:

VariantEffectΔscore
8:27649700:A:AGacceptor_gain1.0000
8:27649701:G:GGacceptor_gain1.0000
8:27649701:GT:Gacceptor_gain1.0000
8:27649796:GAAGG:Gdonor_gain1.0000
8:27649799:GG:Gdonor_gain1.0000
8:27649800:GG:Gdonor_gain1.0000
8:27651503:CACA:Cacceptor_loss1.0000
8:27651505:CA:Cacceptor_loss1.0000
8:27651506:A:AGacceptor_gain1.0000
8:27651506:AGGCC:Aacceptor_gain1.0000
8:27651507:G:GGacceptor_gain1.0000
8:27651507:GGCCG:Gacceptor_gain1.0000
8:27651626:GG:Gdonor_gain1.0000
8:27651626:GGGT:Gdonor_loss1.0000
8:27651627:GG:Gdonor_gain1.0000
8:27651627:GGTG:Gdonor_loss1.0000
8:27651628:G:Adonor_loss1.0000
8:27651629:T:Adonor_loss1.0000
8:27651630:G:GTdonor_loss1.0000
8:27656780:A:AGacceptor_gain1.0000
8:27656781:G:GGacceptor_gain1.0000
8:27659536:CGAG:Cdonor_loss1.0000
8:27659537:GAGG:Gdonor_loss1.0000
8:27659538:AGG:Adonor_loss1.0000
8:27659540:GT:Gdonor_loss1.0000
8:27634207:GGTAA:Gdonor_loss0.9900
8:27634208:GTAA:Gdonor_loss0.9900
8:27649699:TA:Tacceptor_loss0.9900
8:27649699:TAGTG:Tacceptor_gain0.9900
8:27649700:AGT:Aacceptor_gain0.9900

AlphaMissense

3921 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:27659266:G:CA366P0.992
8:27659294:T:CL375P0.982
8:27659323:T:CC385R0.981
8:27659325:C:GC385W0.981
8:27659303:T:CL378P0.980
8:27659102:T:CL311P0.978
8:27659366:T:CL399P0.977
8:27659324:G:AC385Y0.975
8:27659183:G:CR338P0.974
8:27659069:T:CL300P0.973
8:27659315:G:CR382P0.973
8:27659462:T:CL431P0.968
8:27659216:G:CR349P0.965
8:27671161:G:AG544E0.964
8:27659279:A:CH370P0.962
8:27671097:G:CG523R0.960
8:27656784:T:CF77L0.957
8:27656786:C:AF77L0.957
8:27656786:C:GF77L0.957
8:27659282:T:AV371E0.955
8:27659323:T:AC385S0.955
8:27659324:G:CC385S0.955
8:27671116:G:AG529E0.955
8:27658913:T:CL248P0.954
8:27659300:A:GY377C0.954
8:27659261:T:GI364S0.953
8:27659270:C:TT367I0.952
8:27671106:G:CG526R0.952
8:27659292:G:AM374I0.950
8:27659292:G:CM374I0.950

dbSNP variants (sampled 300 via entrez): RS1000009761 (8:27729011 G>A), RS1000013473 (8:27644787 G>A,T), RS1000038334 (8:27690858 T>C), RS1000080967 (8:27650238 G>A), RS1000111479 (8:27719536 T>C,G), RS1000166640 (8:27665103 G>A), RS1000179054 (8:27680262 G>A,C,T), RS1000232848 (8:27679913 T>C,G), RS1000257045 (8:27656096 C>T), RS1000309487 (8:27656343 G>A), RS1000320917 (8:27724650 T>C), RS1000326158 (8:27702244 G>A), RS1000366011 (8:27684991 G>T), RS1000440647 (8:27702458 A>C), RS1000455053 (8:27668402 C>T)

Disease associations

OMIM: gene MIM:602728 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004521_193Autism spectrum disorder or schizophrenia3.000000e-09
GCST010002_272Refractive error3.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

61 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, increases methylation7
Particulate Matterincreases response to substance, affects cotreatment, decreases expression, increases abundance, affects expression (+2 more)4
bisphenol Aaffects expression, decreases expression, affects cotreatment3
sodium arseniteaffects expression, decreases expression, increases expression3
Benzo(a)pyreneincreases expression, affects methylation, decreases expression3
methylmercuric chloridedecreases expression, increases expression2
cobaltous chloridedecreases expression2
(+)-JQ1 compounddecreases expression, increases expression2
Air Pollutantsaffects expression, affects methylation, decreases expression, increases abundance2
Dexamethasonedecreases expression, affects cotreatment2
Tobacco Smoke Pollutiondecreases expression2
pirinixic acidaffects binding, decreases expression, increases activity1
mono-(2-ethylhexyl)phthalatedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
zinc chloridedecreases expression1
butyraldehydedecreases expression1
cerous chloridedecreases expression1
lanthanum chlorideincreases expression1
hydroquinonedecreases expression1
isobutyl alcoholaffects cotreatment, increases abundance, increases expression1
diallyl trisulfidedecreases expression1
avobenzoneincreases expression1
perfluoro-n-nonanoic aciddecreases expression1
2-palmitoylglycerolincreases expression1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.