SCART1

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 be involved in T cell mediated immunity. Located in brush border and cytoplasm.

Source: NCBI Gene 619207 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001396050

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32411
Approved symbol	SCART1
Name	scavenger receptor family member expressed on T cells 1
Location	10q26.3
Locus type	gene with protein product
Status	Approved
Aliases	CD163c-alpha
Ensembl gene	ENSG00000214279
Ensembl biotype	protein_coding
Entrez	619207

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 retained_intron, 1 protein_coding

ENST00000462252, ENST00000463137, ENST00000475114, ENST00000482993, ENST00000488261, ENST00000640237

RefSeq mRNA: 1 — MANE Select: NM_001396050 NM_001396050

CCDS: CCDS91391

Canonical transcript exons

ENST00000640237 — 12 exons

Exon	Start	End
ENSE00001628808	133457279	133457575
ENSE00003802017	133459021	133459326
ENSE00003803573	133456237	133456554
ENSE00003805075	133458360	133458656
ENSE00003805472	133466235	133466381
ENSE00003805698	133459487	133460170
ENSE00003806019	133465106	133465174
ENSE00003807120	133465251	133465565
ENSE00003807709	133464606	133464911
ENSE00003809737	133467198	133467353
ENSE00003978156	133467847	133469760
ENSE00003978157	133453945	133454064

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.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107803	0.3060	88
107802	0.0171	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	81.95	gold quality
lower esophagus mucosa	UBERON:0035834	79.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.04	gold quality
stromal cell of endometrium	CL:0002255	73.53	gold quality
esophagus mucosa	UBERON:0002469	72.14	gold quality
right adrenal gland cortex	UBERON:0035827	71.76	gold quality
body of pancreas	UBERON:0001150	71.39	gold quality
body of uterus	UBERON:0009853	70.99	gold quality
body of stomach	UBERON:0001161	70.95	gold quality
granulocyte	CL:0000094	70.85	gold quality
right adrenal gland	UBERON:0001233	70.38	gold quality
popliteal artery	UBERON:0002250	70.21	gold quality
tibial artery	UBERON:0007610	70.21	gold quality
esophagus	UBERON:0001043	70.15	gold quality
muscle layer of sigmoid colon	UBERON:0035805	70.09	gold quality
right lobe of liver	UBERON:0001114	70.04	gold quality
left adrenal gland cortex	UBERON:0035825	69.37	gold quality
metanephros cortex	UBERON:0010533	69.28	gold quality
spleen	UBERON:0002106	69.24	gold quality
aorta	UBERON:0000947	69.20	gold quality
sural nerve	UBERON:0015488	69.14	gold quality
left lobe of thyroid gland	UBERON:0001120	69.03	gold quality
skin of abdomen	UBERON:0001416	68.86	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	68.83	gold quality
left adrenal gland	UBERON:0001234	68.61	gold quality
bone marrow cell	CL:0002092	68.55	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	68.46	gold quality
left coronary artery	UBERON:0001626	68.45	gold quality
right frontal lobe	UBERON:0002810	68.45	gold quality
lower esophagus	UBERON:0013473	68.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.29

Regulation

Is transcription factor: no

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

Organism	Symbol	Gene ID
mus_musculus	Scart2	ENSMUSG00000054672
rattus_norvegicus	Or12j2	ENSRNOG00000036647

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)

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 ID	Names	Canonical?
Q4G0T1-1	1	yes
Q4G0T1-2	Gamma
Q4G0T1-3	Alpha

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

Domains & families (InterPro)

ID	Name	Type
IPR001190	SRCR	Domain
IPR036772	SRCR-like_dom_sf	Homologous_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

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4G0T1-F1	70.15	0.17

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): 53–117, 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): 94, 129, 332

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

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 (2): T cell mediated immunity (GO:0002456), immune system process (GO:0002376)

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
lymphocyte mediated immunity	1
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	1
biological_process	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
microvillus	1
apical part of cell	1
cluster of actin-based cell projections	1

Protein interactions and networks

STRING

532 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCART1	OR7A17	O14581	479
SCART1	FUOM	A2VDF0	420
SCART1	CYP4V2	Q6ZWL3	364
SCART1	LDLRAD2	Q5SZI1	359
SCART1	CD5	P06127	352
SCART1	SOX13	Q9UN79	308
SCART1	HP	P00737	290
SCART1	FHOD1	Q9Y613	286
SCART1	BMP1	P13497	282
SCART1	HPR	P00739	273
SCART1	IL17A	Q16552	272
SCART1	TLL1	O43897	254
SCART1	PRAP1	Q96NZ9	250
SCART1	IL2RB	P14784	245
SCART1	CCR6	P51684	238

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GPC3	PXDNL	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A1L0T3, A1L4H1, D3ZTE0, G3V801, O08762, O43866, O75636, O95428, O97507, P00748, P22457, P56730, P58215, P69525, P69526, P85521, P98140, Q02853, Q04756, Q04962, Q24K22, Q2VL90, Q2VLG4, Q2VLG6, Q2VLH6, Q499S5, Q4G0T1, Q5G265, Q5G268, Q5G269, Q5G270, Q5G271, Q5IJ48, Q6QNF4, Q70UZ7, Q769J6, Q76LX8, Q7Z410, Q80YA8, Q80YC5

Diamond homologs: A1L0T3, A1L1V4, A1L4H1, A5PJQ2, A6H737, A7E3W2, B4F6N6, B5DF27, B8A4W9, E1C3U7, F1QQC3, F1RD85, F7J220, G3V801, M9NDE3, O08762, O43866, O70513, P21757, P21758, P30203, P30204, P30205, P56730, P58022, P58215, P70117, P85521, Q05585, Q07797, Q08380, Q08B63, Q14DK5, Q24JV9, Q2VL90, Q2VLG4, Q2VLG6, Q2VLH6, Q4A3R3, Q4G0T1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

171 predictions. Top by Δscore:

Variant	Effect	Δscore
10:133520550:G:GT	donor_gain	0.9700
10:133520557:C:T	donor_gain	0.9600
10:133520630:TG:T	donor_gain	0.9600
10:133520653:A:G	donor_gain	0.9600
10:133520479:G:GT	donor_gain	0.9500
10:133520631:G:GT	donor_gain	0.9500
10:133520715:G:GT	donor_gain	0.9500
10:133520561:GTT:G	donor_gain	0.9400
10:133520562:T:G	donor_gain	0.9400
10:133520631:GA:G	donor_gain	0.9400
10:133520632:AA:A	donor_gain	0.9400
10:133520557:CGAG:C	donor_loss	0.9300
10:133520558:GAGG:G	donor_loss	0.9300
10:133520560:GGTTG:G	donor_loss	0.9300
10:133520561:GTTGT:G	donor_loss	0.9300
10:133520512:G:GT	donor_gain	0.9200
10:133520629:GTGAA:G	donor_gain	0.9100
10:133520513:G:GT	donor_gain	0.9000
10:133520513:G:T	donor_gain	0.9000
10:133521014:TC:T	donor_gain	0.8900
10:133520510:C:T	donor_gain	0.8800
10:133520558:G:GT	donor_gain	0.8600
10:133520634:G:GG	donor_gain	0.8500
10:133520533:GC:G	donor_gain	0.8400
10:133520617:T:TA	donor_gain	0.8300
10:133521010:G:T	donor_gain	0.8200
10:133520633:A:AG	donor_gain	0.8000
10:133520618:C:CA	donor_gain	0.7900
10:133520620:T:G	donor_gain	0.7800
10:133520628:A:AG	donor_gain	0.7800

AlphaMissense

6543 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:133456340:G:C	W57C	0.998
10:133456340:G:T	W57C	0.998
10:133459112:G:C	W357C	0.996
10:133459112:G:T	W357C	0.996
10:133459590:G:C	W463C	0.994
10:133459590:G:T	W463C	0.994
10:133456338:T:A	W57R	0.993
10:133456338:T:C	W57R	0.993
10:133458424:G:C	W249C	0.988
10:133458424:G:T	W249C	0.988
10:133459566:G:C	W455C	0.986
10:133459566:G:T	W455C	0.986
10:133456367:C:G	C66W	0.984
10:133457406:C:G	C171W	0.984
10:133459738:T:A	C513S	0.984
10:133459739:G:C	C513S	0.984
10:133456365:T:A	C66S	0.983
10:133456366:G:A	C66Y	0.983
10:133456366:G:C	C66S	0.983
10:133457405:G:A	C171Y	0.983
10:133458550:G:C	W291C	0.983
10:133458550:G:T	W291C	0.983
10:133459137:T:A	C366S	0.983
10:133459138:G:C	C366S	0.983
10:133456458:T:A	C97S	0.981
10:133456459:G:C	C97S	0.981
10:133458566:T:A	C297S	0.981
10:133458567:G:C	C297S	0.981
10:133456380:T:A	C71S	0.980
10:133456381:G:C	C71S	0.980

dbSNP variants (sampled 300 via entrez): RS1000042474 (10:133463850 G>A), RS1000191074 (10:133469190 G>A,C), RS1000263474 (10:133461205 G>A,C), RS1000441425 (10:133456833 C>A,G,T), RS1000499098 (10:133464277 G>A,T), RS1000763004 (10:133453666 G>A), RS1000802462 (10:133457069 G>C), RS1000871510 (10:133453866 G>A,T), RS1001231008 (10:133456801 G>A), RS1001344040 (10:133452470 T>G), RS1001438952 (10:133460799 T>G), RS1001558355 (10:133465968 C>A), RS1001822574 (10:133456417 T>C), RS1001853926 (10:133456541 C>T), RS1002602567 (10:133465961 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
fipronil	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
Fulvestrant	affects cotreatment, decreases methylation	1
DEET	affects cotreatment, decreases expression	1
Endosulfan	decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Smoke	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases expression	1
Permethrin	increases expression	1

Clinical trials (associated diseases)

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