Send feedback

SCART1

gene
On this page

Also known as CD163c-alpha

Summary

SCART1 (scavenger receptor family member expressed on T cells 1, HGNC:32411) is a protein-coding gene on chromosome 10q26.3, encoding Scavenger receptor cysteine-rich domain-containing protein SCART1 (Q4G0T1). May play a role in the immune system, perhaps as a co-receptor on alphabeta and gammadelta T-cells.

Predicted to enable scavenger receptor activity. Predicted to be involved in gamma-delta T cell lineage commitment. Located in brush border and cytoplasm.

Source: NCBI Gene 619207 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • GTEx eGene: eQTL in 46 tissues, sQTL in 16 (q < 0.05)
  • MANE Select transcript: NM_001396050

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:32411
Approved symbolSCART1
Namescavenger receptor family member expressed on T cells 1
Location10q26.3
Locus typegene with protein product
StatusApproved
AliasesCD163c-alpha
Ensembl geneENSG00000214279
Ensembl biotypeprotein_coding
Entrez619207

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 retained_intron, 2 protein_coding

MANE Select: ENST00000640237

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 5, TSL 5: 1

ENST00000640237, ENST00000462252, ENST00000463137, ENST00000475114, ENST00000482993, ENST00000488261, ENST00001136530

RefSeq mRNA: 1 — MANE Select: NM_001396050 NM_001396050

CCDS: CCDS91391

Canonical transcript exons

ENST00000640237 — 12 exons

ExonStartEnd
ENSE00001628808133457279133457575
ENSE00003802017133459021133459326
ENSE00003803573133456237133456554
ENSE00003805075133458360133458656
ENSE00003805472133466235133466381
ENSE00003805698133459487133460170
ENSE00003806019133465106133465174
ENSE00003807120133465251133465565
ENSE00003807709133464606133464911
ENSE00003809737133467198133467353
ENSE00003978156133467847133469760
ENSE00003978157133453945133454064

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 81.95.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3231 / max 66.2479, expressed in 89 samples.

Highest expression (Bgee): uterine tube, lower esophagus mucosa, male germ line stem cell (sensu Vertebrata) in testis, stromal cell of endometrium, esophagus mucosa.

Genetic regulation across tissues (GTEx eQTL / sQTL)

SCART1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 46 tissues and its splicing (sQTL) in 16 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 62 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Nerve Tibialeqtl1.8e-22-0.4410:133419150:C:T
Testiseqtl4.1e-20-0.5710:133419150:C:T
Pituitaryeqtl2.0e-19-0.7010:133419150:C:T
Brain Frontal Cortex BA9eqtl5.0e-17-0.6210:133429144:C:CAG
Thyroideqtl7.5e-17-0.3710:133411456:A:G
Brain Cortexeqtl4.4e-16+0.6710:133449883:A:G
Brain Nucleus accumbens basal gangliaeqtl2.8e-15+0.5610:133429369:G:A
Brain Caudate basal gangliaeqtl2.4e-14-0.4910:133419150:C:T
Lungeqtl1.5e-13-0.3310:133411456:A:G
Brain Hypothalamuseqtl4.3e-12-0.4510:133421866:C:A
Adrenal Glandeqtl6.2e-12-0.5710:133403471:G:A
Adipose Subcutaneouseqtl8.7e-12-0.6510:133463654:G:A
Cells Cultured fibroblastseqtl8.9e-12-0.3110:133419150:C:T
Brain Cerebellumeqtl3.6e-11-0.6110:133419150:C:T
Testissqtl7.0e-11+0.7810:133469269:T:G
Artery Tibialsqtl9.1e-11+0.4510:133419150:C:T
Brain Anterior cingulate cortex BA24eqtl9.8e-11+0.4910:133419430:C:T
Artery Tibialeqtl3.1e-10-0.5010:133458260:G:A
Muscle Skeletaleqtl5.6e-10-0.5510:133397517:C:T
Adipose Visceral Omentumeqtl1.1e-09-0.3410:133411456:A:G

FANTOM5 promoters

2 alternative TSS:

Promoter IDTPM avgSamples expressed
1078030.306088
1078020.01715

Top tissues by expression

showing 100 of 246 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130281.95gold quality
lower esophagus mucosaUBERON:003583479.98gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047374.04gold quality
stromal cell of endometriumCL:000225573.53gold quality
esophagus mucosaUBERON:000246972.14gold quality
right adrenal gland cortexUBERON:003582771.76gold quality
body of pancreasUBERON:000115071.39gold quality
body of uterusUBERON:000985370.99gold quality
body of stomachUBERON:000116170.95gold quality
granulocyteCL:000009470.85gold quality
right adrenal glandUBERON:000123370.38gold quality
popliteal arteryUBERON:000225070.21gold quality
tibial arteryUBERON:000761070.21gold quality
esophagusUBERON:000104370.15gold quality
muscle layer of sigmoid colonUBERON:003580570.09gold quality
right lobe of liverUBERON:000111470.04gold quality
left adrenal gland cortexUBERON:003582569.37gold quality
metanephros cortexUBERON:001053369.28gold quality
spleenUBERON:000210669.24gold quality
aortaUBERON:000094769.20gold quality
sural nerveUBERON:001548869.14gold quality
left lobe of thyroid glandUBERON:000112069.03gold quality
skin of abdomenUBERON:000141668.86gold quality
esophagogastric junction muscularis propriaUBERON:003584168.83gold quality
left adrenal glandUBERON:000123468.61gold quality
bone marrow cellCL:000209268.55gold quality
C1 segment of cervical spinal cordUBERON:000646968.46gold quality
left coronary arteryUBERON:000162668.45gold quality
right frontal lobeUBERON:000281068.45gold quality
lower esophagusUBERON:001347368.40gold quality
lower esophagus muscularis layerUBERON:003583368.37gold quality
thoracic aortaUBERON:000151568.24gold quality
ascending aortaUBERON:000149668.20gold quality
right coronary arteryUBERON:000162568.08gold quality
left uterine tubeUBERON:000130368.05gold quality
minor salivary glandUBERON:000183068.03gold quality
right ovaryUBERON:000211867.82gold quality
adrenal cortexUBERON:000123567.80gold quality
right lobe of thyroid glandUBERON:000111967.71gold quality
skin of legUBERON:000151167.70gold quality
small intestine Peyer’s patchUBERON:000345467.56gold quality
ectocervixUBERON:001224967.54gold quality
transverse colonUBERON:000115767.46gold quality
stomachUBERON:000094567.30gold quality
descending thoracic aortaUBERON:000234567.19gold quality
thyroid glandUBERON:000204667.17gold quality
endocervixUBERON:000045867.10gold quality
coronary arteryUBERON:000162166.89gold quality
tibial nerveUBERON:000132366.83gold quality
gall bladderUBERON:000211066.67gold quality
left ovaryUBERON:000211966.60gold quality
hindlimb stylopod muscleUBERON:000425266.50gold quality
colonic epitheliumUBERON:000039766.45silver quality
mucosa of stomachUBERON:000119966.20gold quality
spinal cordUBERON:000224065.90gold quality
omental fat padUBERON:001041465.73gold quality
peritoneumUBERON:000235865.66gold quality
Brodmann (1909) area 9UBERON:001354065.65gold quality
adrenal glandUBERON:000236965.35gold quality
small intestineUBERON:000210865.33gold quality
right hemisphere of cerebellumUBERON:001489065.15gold quality
right lungUBERON:000216765.04gold quality
zone of skinUBERON:000001465.03gold quality
upper lobe of left lungUBERON:000895265.03gold quality
cortex of kidneyUBERON:000122564.77gold quality
uterine cervixUBERON:000000264.72gold quality
mouth mucosaUBERON:000372964.45gold quality
adenohypophysisUBERON:000219664.43gold quality
adipose tissue of abdominal regionUBERON:000780864.38gold quality
saliva-secreting glandUBERON:000104464.21gold quality
gastrocnemiusUBERON:000138864.13gold quality
pituitary glandUBERON:000000764.07gold quality
muscle of legUBERON:000138364.00gold quality
smooth muscle tissueUBERON:000113563.99gold quality
colonUBERON:000115563.80gold quality
cerebellar hemisphereUBERON:000224563.77gold quality
vaginaUBERON:000099663.67gold quality
apex of heartUBERON:000209863.66gold quality
cerebellar cortexUBERON:000212963.66gold quality
fundus of stomachUBERON:000116063.52gold quality
upper lobe of lungUBERON:000894863.46gold quality
intestineUBERON:000016063.28gold quality
vermiform appendixUBERON:000115463.22gold quality
large intestineUBERON:000005962.99gold quality
subcutaneous adipose tissueUBERON:000219062.54gold quality
prostate glandUBERON:000236762.29gold quality
ovaryUBERON:000099262.22gold quality
cerebellumUBERON:000203762.07gold quality
mucosa of transverse colonUBERON:000499162.00gold quality
lymph nodeUBERON:000002961.85gold quality
rectumUBERON:000105261.84gold quality
anterior cingulate cortexUBERON:000983561.70gold quality
right atrium auricular regionUBERON:000663161.64gold quality
endothelial cellCL:000011561.53gold quality
pancreasUBERON:000126461.53gold quality
heart left ventricleUBERON:000208461.24gold quality
Ammon’s hornUBERON:000195461.23gold quality
anatomical systemUBERON:000046761.16gold quality
cardiac atriumUBERON:000208161.10gold quality
liverUBERON:000210760.90gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no4.29

HPA expression

RNA tissue specificity: Low tissue specificity

43 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Hippocampustissue13.4not detected
Postcentral gyrustissue9.6
Choroid plexustissue7.6
Nucleus accumbenstissue7.5
Locus coeruleustissue6.3
Skin 1tissue0.8not detected
Bone marrowtissue0.8not detected
Epididymistissue0.7not detected
Spleentissue0.7medium
Retinatissue0.6
Breasttissue0.5not detected
Skeletal muscletissue0.5not detected
Livertissue0.5not detected
Small intestinetissue0.5not detected
Duodenumtissue0.5not detected
Lymph nodetissue0.4medium
Testistissue0.3not detected
Stomach 1tissue0.3not detected
Adipose tissuetissue0.3not detected
Lungtissue0.3low
Appendixtissue0.3not detected
Salivary glandtissue0.2not detected
Rectumtissue0.2not detected
Colontissue0.2not detected
Pancreastissue0.2not detected
Endometrium 1tissue0.2not detected
Placentatissue0.2not detected
Gallbladdertissue0.2not detected
Kidneytissue0.2not detected
Prostatetissue0.2not detected
Adrenal glandtissue0.2not detected
Tonsiltissue0.2medium
Cervixtissue0.1not detected
Pituitary glandtissue0.1
Heart muscletissue0.1not detected
Ovarytissue0.1not detected
Seminal vesicletissue0.1not detected
Esophagustissue0.1not detected
Parathyroid glandtissue0.1not detected
Smooth muscletissue0.1not detected
Thyroid glandtissue0.1not detected
Thymustissue0.1
Fallopian tubetissue0.1not detected

Brain sub-regions (HPA Brain Atlas): detected in 183; highest nTPM — Posterior cingulate cortex (17.7), Hippocampus, CA3 (17.6), Dentate gyrus (13.6), Hippocampus, CA1 (13.1), Flocculonodular lobe (11.8).

Regulation

Is transcription factor: no

Functional genomics

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000640237 — one region, missense o/e 1.93.

Literature-anchored findings (GeneRIF, showing 1)

  • the characterization of hSCART1 at the mRNA and protein level suggests that the protein plays a role in the immune system, perhaps as a co-receptor on alphabeta and gammadelta T cells. (PMID:22795646)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusScart1ENSMUSG00000025461
rattus_norvegicusScart1ENSRNOG00000018978

Paralogs (15): CD6 (ENSG00000013725), CD5L (ENSG00000073754), LGALS3BP (ENSG00000108679), CD5 (ENSG00000110448), LOX (ENSG00000113083), LOXL3 (ENSG00000115318), LOXL1 (ENSG00000129038), LOXL2 (ENSG00000134013), LOXL4 (ENSG00000138131), SSC4D (ENSG00000146700), PRSS12 (ENSG00000164099), CD163 (ENSG00000177575), CD163L1 (ENSG00000177675), SSC5D (ENSG00000179954), DMBT1 (ENSG00000187908)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Pongo abeliiQ5RDA499.5%Diamond
Pan troglodytesQ5G27199.2%Diamond
Nomascus leucogenysQ5G26898.5%Diamond
Gorilla gorilla gorillaQ5G27098.5%Diamond
Trachypithecus phayreiQ5G26698.3%Diamond
Macaca mulattaQ5G26798.3%Diamond
Pongo pygmaeusQ5G26996.7%Diamond
Chlorocebus aethiopsQ2VLG495.8%Diamond
Saguinus labiatusQ5G26595.5%Diamond
Bos taurusA6H73792.9%Diamond
Xenopus tropicalisB4F6N691.4%Diamond
Xenopus laevisQ08B6391.4%Diamond
Sus scrofaQ2VL9084.0%Diamond
Canis lupus familiarisQ2VLG684.0%Diamond
Mesocricetus auratusP7011782.3%Diamond
Gallus gallusE1C3U779.4%Diamond
Danio rerioQ24JV978.8%Diamond
Oryctolagus cuniculusQ0558578.4%Diamond
Patiria pectiniferaF7J22054.5%Diamond
Drosophila melanogasterM9NDE341.9%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
CYP2E1protein-coding1571
SYCE1protein-coding93426
PAOXprotein-coding196743
SPRNprotein-coding503542
MTG1protein-coding92170

Protein

Protein identifiers

Scavenger receptor cysteine-rich domain-containing protein SCART1 — Q4G0T1 (reviewed: Q4G0T1)

Alternative names: Scavenger receptor family member expressed on T cells 1

All UniProt accessions (1): Q4G0T1

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the immune system, perhaps as a co-receptor on alphabeta and gammadelta T-cells.

Subcellular location. Membrane.

Tissue specificity. Mainly expressed by CD4(+) and CD8(+) T lymphocytes. Also highly expressed in small intestine and colon. Expressed (at protein level) in small intestine, stomach, gall bladder, and placental villi.

Isoforms (3)

UniProt IDNamesCanonical?
Q4G0T1-11yes
Q4G0T1-2Gamma
Q4G0T1-3Alpha

RefSeq proteins (1): NP_001382979* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001190SRCRDomain
IPR036772SRCR-like_dom_sfHomologous_superfamily

Pfam: PF00530

UniProt features (40 total): disulfide bond 18, domain 8, splice variant 4, glycosylation site 3, topological domain 2, sequence conflict 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4G0T1-F170.150.17

Human Protein Atlas

Protein class: Predicted membrane proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH supported

Functional residue map

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

Disulfide bonds (18)

TypePositions
Disulfide bond53–117, 66–127, 97–107, 160–216, 171–226, 196–206, 253–315, 266–325, 297–307, 353–417, 366–427, 397–407, 472–533, 503–513, 594–655, 625–635, 824–885, 855–865

Glycosylation sites (3)

TypePositions
N-linked (glcnac…) asparagine94, 129, 332

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 51 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, CADWELL_ATG16L1_TARGETS_DN, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, GOBP_ADAPTIVE_IMMUNE_RESPONSE, GOBP_IMMUNE_EFFECTOR_PROCESS, GOBP_T_CELL_LINEAGE_COMMITMENT, GOBP_T_CELL_MEDIATED_IMMUNITY, GOBP_CELL_FATE_COMMITMENT, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_ADAPTIVE_IMMUNE_RESPONSE_BASED_ON_SOMATIC_RECOMBINATION_OF_IMMUNE_RECEPTORS_BUILT_FROM_IMMUNOGLOBULIN_SUPERFAMILY_DOMAINS, GOCC_APICAL_PART_OF_CELL, GAVIN_FOXP3_TARGETS_CLUSTER_T7, GAVIN_FOXP3_TARGETS_CLUSTER_P3, GOCC_CLUSTER_OF_ACTIN_BASED_CELL_PROJECTIONS

GO Biological Process (4): gamma-delta T cell lineage commitment (GO:0002365), T cell mediated immunity (GO:0002456), immune system process (GO:0002376), vesicle-mediated transport (GO:0016192)

GO Molecular Function (1): scavenger receptor activity (GO:0005044)

GO Cellular Component (4): cytoplasm (GO:0005737), plasma membrane (GO:0005886), brush border (GO:0005903), membrane (GO:0016020)

GO top-level categories

15 GO namespaces:

CategoryTerms
cellular anatomical structure2
T cell lineage commitment1
gamma-delta T cell differentiation1
lymphocyte mediated immunity1
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains1
biological_process1
transport1
cellular process1
cargo receptor activity1
intracellular anatomical structure1
membrane1
cell periphery1
microvillus1
apical part of cell1
cluster of actin-based cell projections1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO termNSEvidence
brush borderCCdirect assay
cytoplasmCCdirect assay

Protein interactions and networks

STRING

showing 15 of 262 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCART1SYCE1Q8N0S2389
SCART1OR7A17O14581384
SCART1FHOD1Q9Y613356
SCART1EFCAB14O75071340
SCART1SOX13Q9UN79338
SCART1BMP1P13497321
SCART1GP2P55259301
SCART1CD151P48509297
SCART1FUOMA2VDF0295
SCART1LDLRAD2Q5SZI1285
SCART1CD5P06127277
SCART1TEX101Q9BY14271
SCART1GK3Q14409260
SCART1SCARF2Q96GP6241
SCART1CASKIN2Q8WXE0240

Disease & clinical

Genetic variants

ClinVar

No ClinVar records for this gene.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 1,016):

Position(s)EffectΔscoreSites
10:133467196–133467197acceptor_loss1.00002
10:133467354–133467355donor_loss1.00005
10:133454065–133454066donor_loss0.99005
10:133457576–133457577donor_loss0.99005
10:133459485–133459486acceptor_loss0.99006
10:133460171–133460172donor_loss0.99005
10:133467196–133467197acceptor_loss0.99003
10:133467355donor_loss0.9800
10:133467774acceptor_gain0.9800
10:133467358donor_gain0.9600

AlphaMissense

1,378 missense substitutions predicted likely pathogenic (of 6,543 scored), across 388 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
F17080.8120.970
D3880.8060.915
D52880.7540.856
C6670.9630.984
C36670.9600.983
C17170.9590.984
W5770.9550.998
C9770.9550.981
C5370.9530.977
C20670.9490.973
C22670.9470.976
C7170.9460.980
C29770.9450.981
C12770.9440.978
C39770.9430.976
C51370.9430.984
C17670.9410.979
C19670.9400.972
C3770.9390.963
C40770.9370.963

HPA cancer prognostics

RNA cancer specificity: Not detected

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

CancerPrognosticp-value
Glioblastoma Multiforme (validation)favorable2.87e-05

Disease associations

OMIM: gene `` | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, decreases methylation1
fipronilaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
Fulvestrantaffects cotreatment, decreases methylation1
DEETdecreases expression, affects cotreatment1
Endosulfandecreases expression1
N-Nitrosopyrrolidinedecreases expression1
Smokeincreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1decreases expression1
Permethrinincreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

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