SSC4D

Summary

SSC4D (scavenger receptor cysteine rich family member with 4 domains, HGNC:14461) is a protein-coding gene on chromosome 7q11.23, encoding Scavenger receptor cysteine-rich domain-containing group B protein (Q8WTU2).

The scavenger receptor cysteine-rich (SRCR) superfamily is an ancient and highly conserved group of cell surface and/or secreted proteins, some of which are involved in the development of the immune system and the regulation of both innate and adaptive immune responses. Group B SRCR domains usually contain 8 regularly spaced cysteines that give rise to a well-defined intradomain disulfide-bond pattern.

Source: NCBI Gene 136853 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_080744

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14461
Approved symbol	SSC4D
Name	scavenger receptor cysteine rich family member with 4 domains
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Aliases	SRCRB-S4D, S4D-SRCRB
Ensembl gene	ENSG00000146700
Ensembl biotype	protein_coding
OMIM	607639
Entrez	136853

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000275560, ENST00000492979, ENST00000938539, ENST00000938540, ENST00000938541, ENST00000938542, ENST00000938543, ENST00000938544, ENST00000938545

RefSeq mRNA: 1 — MANE Select: NM_080744 NM_080744

CCDS: CCDS5585

Canonical transcript exons

ENST00000275560 — 11 exons

Exon	Start	End
ENSE00000976851	76397518	76397832
ENSE00000976854	76400286	76400591
ENSE00001090383	76395253	76395330
ENSE00001090416	76393830	76393904
ENSE00001090430	76398720	76398797
ENSE00001127672	76404307	76404505
ENSE00001146417	76401008	76401043
ENSE00001146426	76409414	76409697
ENSE00001200262	76393405	76393716
ENSE00003492885	76391964	76392041
ENSE00003511903	76389337	76390375

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 94.33.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9562 / max 115.0544, expressed in 280 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
84440	1.6909	264
84439	0.2653	119

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	94.33	silver quality
parotid gland	UBERON:0001831	87.44	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.89	gold quality
kidney epithelium	UBERON:0004819	86.72	gold quality
upper arm skin	UBERON:0004263	84.46	gold quality
epithelial cell of pancreas	CL:0000083	82.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.50	gold quality
cerebellar vermis	UBERON:0004720	79.66	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	79.52	silver quality
tendon of biceps brachii	UBERON:0008188	77.55	gold quality
middle temporal gyrus	UBERON:0002771	77.07	silver quality
vena cava	UBERON:0004087	76.27	silver quality
deltoid	UBERON:0001476	76.01	silver quality
tibialis anterior	UBERON:0001385	75.94	silver quality
left ventricle myocardium	UBERON:0006566	75.62	gold quality
endothelial cell	CL:0000115	74.71	gold quality
dorsal plus ventral thalamus	UBERON:0001897	74.42	silver quality
cardiac muscle of right atrium	UBERON:0003379	74.15	gold quality
pons	UBERON:0000988	74.12	silver quality
medial globus pallidus	UBERON:0002477	74.02	silver quality
substantia nigra pars compacta	UBERON:0001965	73.88	silver quality
lateral globus pallidus	UBERON:0002476	73.53	silver quality
buccal mucosa cell	CL:0002336	73.32	silver quality
metanephros cortex	UBERON:0010533	73.31	gold quality
metanephros	UBERON:0000081	73.29	gold quality
pharyngeal mucosa	UBERON:0000355	73.28	silver quality
saphenous vein	UBERON:0007318	73.06	silver quality
pericardium	UBERON:0002407	72.92	silver quality
skeletal muscle tissue	UBERON:0001134	72.71	gold quality
sperm	CL:0000019	72.54	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting SSC4D, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-548Q	98.71	65.35	563
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-4443	98.02	66.25	1928

Literature-anchored findings (GeneRIF, showing 3)

• Cloning of S4D-SRCRB, a new soluble member of the group B scavenger receptor cysteine-rich family (SRCR-SF) mapping to human chromosome 7q11.23. (PMID:12466895)
• SRCRB4D is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells. (PMID:21555518)
• Physical Interactions With Bacteria and Protozoan Parasites Establish the Scavenger Receptor SSC4D as a Broad-Spectrum Pattern Recognition Receptor. (PMID:35003072)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ssc4d	ENSMUSG00000029699
rattus_norvegicus	Ssc4d	ENSRNOG00000001435

Paralogs (15): CD6 (ENSG00000013725), CD5L (ENSG00000073754), LGALS3BP (ENSG00000108679), CD5 (ENSG00000110448), LOX (ENSG00000113083), LOXL3 (ENSG00000115318), LOXL1 (ENSG00000129038), LOXL2 (ENSG00000134013), LOXL4 (ENSG00000138131), PRSS12 (ENSG00000164099), CD163 (ENSG00000177575), CD163L1 (ENSG00000177675), SSC5D (ENSG00000179954), DMBT1 (ENSG00000187908), SCART1 (ENSG00000214279)

Protein

Protein identifiers

Scavenger receptor cysteine-rich domain-containing group B protein — Q8WTU2 (reviewed: Q8WTU2)

Alternative names: Four scavenger receptor cysteine-rich domains-containing protein, S4D-SRCRB

All UniProt accessions (1): Q8WTU2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Induction. Not induced by a combination of IL1A/interleukin-1 alpha, IL6/interleukin-6 and dexamethasone.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WTU2-1	1	yes
Q8WTU2-2	2

RefSeq proteins (1): NP_542782* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001190	SRCR	Domain
IPR036772	SRCR-like_dom_sf	Homologous_superfamily

Pfam: PF00530

UniProt features (22 total): disulfide bond 12, domain 4, splice variant 2, signal peptide 1, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WTU2-F1	73.06	0.35

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 (12): 227–288, 258–268, 369–433, 382–443, 413–423, 498–562, 511–572, 542–552, 83–147, 96–157, 127–137, 214–278

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_VESICLE_MEDIATED_TRANSPORT, CAGCTG_AP4_Q5, CATRRAGC_UNKNOWN, INAMURA_LUNG_CANCER_SCC_DN, PETRETTO_HEART_MASS_QTL_CIS_DN, HFH4_01, chr7q11, ACEVEDO_LIVER_CANCER_UP, ZAMORA_NOS2_TARGETS_DN, GOMF_SCAVENGER_RECEPTOR_ACTIVITY, GOMF_CARGO_RECEPTOR_ACTIVITY, TTTGCAG_MIR518A2, FORTSCHEGGER_PHF8_TARGETS_DN, FOXD2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): extracellular region (GO:0005576), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2

Protein interactions and networks

STRING

610 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSC4D	FBXO21	O94952	535
SSC4D	FAM222B	Q8WU58	484
SSC4D	FBLN1	P23142	468
SSC4D	ZNF572	Q7Z3I7	437
SSC4D	PLAAT2	Q9NWW9	432
SSC4D	ZNF789	Q5FWF6	416
SSC4D	ZSCAN25	Q6NSZ9	391
SSC4D	FAM177A1	Q8N128	389
SSC4D	LDLRAD2	Q5SZI1	374
SSC4D	TMPRSS15	P98073	365
SSC4D	FAT3	Q8TDW7	365
SSC4D	SRD5A3	Q9H8P0	344
SSC4D	CD5	P06127	343
SSC4D	CLEC18A	A5D8T8	342
SSC4D	SNX21	Q969T3	336

IntAct

11 interactions, top by confidence:

A	B	Type	Score
CMA1	MANBA	psi-mi:“MI:0914”(association)	0.530
EGFL8	MPO	psi-mi:“MI:0914”(association)	0.530
EMILIN3	ZZEF1	psi-mi:“MI:0914”(association)	0.530
SSC4D	TSC2	psi-mi:“MI:0915”(physical association)	0.370
NUDCD1	TUBAL3	psi-mi:“MI:0914”(association)	0.350
NUDCD1	APOBEC3B	psi-mi:“MI:0914”(association)	0.350
NUDCD1	DNAJB2	psi-mi:“MI:0914”(association)	0.350
SSC4D	TOP3A	psi-mi:“MI:0914”(association)	0.350
SSC4D	BCKDK	psi-mi:“MI:0914”(association)	0.350
PRG3	IGLL5	psi-mi:“MI:0914”(association)	0.350

BioGRID (45): SSC4D (Reconstituted Complex), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid), SSC4D (Two-hybrid)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1937 predictions. Top by Δscore:

Variant	Effect	Δscore
7:76391959:CCTA:C	donor_loss	1.0000
7:76391960:CTA:C	donor_loss	1.0000
7:76391961:TA:T	donor_loss	1.0000
7:76391962:A:C	donor_loss	1.0000
7:76391967:C:A	donor_gain	1.0000
7:76392042:C:CC	acceptor_gain	1.0000
7:76392048:C:CT	acceptor_gain	1.0000
7:76392049:A:T	acceptor_gain	1.0000
7:76393828:A:AC	donor_gain	1.0000
7:76393829:C:CC	donor_gain	1.0000
7:76397833:C:CA	acceptor_loss	1.0000
7:76397834:T:A	acceptor_loss	1.0000
7:76398714:A:AC	donor_gain	1.0000
7:76398715:C:CC	donor_gain	1.0000
7:76398715:CGT:C	donor_gain	1.0000
7:76398715:CGTA:C	donor_gain	1.0000
7:76398716:GTA:G	donor_loss	1.0000
7:76398717:TA:T	donor_loss	1.0000
7:76398718:A:AC	donor_gain	1.0000
7:76398719:C:CT	donor_gain	1.0000
7:76398719:CT:C	donor_gain	1.0000
7:76398719:CTT:C	donor_gain	1.0000
7:76398719:CTTT:C	donor_gain	1.0000
7:76398795:ATTC:A	acceptor_loss	1.0000
7:76398796:TT:T	acceptor_gain	1.0000
7:76398797:TCT:T	acceptor_loss	1.0000
7:76398798:C:CC	acceptor_gain	1.0000
7:76398799:T:C	acceptor_loss	1.0000
7:76409409:CATA:C	donor_loss	1.0000
7:76409410:ATAC:A	donor_loss	1.0000

AlphaMissense

3685 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:76393619:C:A	W373C	1.000
7:76393619:C:G	W373C	1.000
7:76397732:C:A	W218C	1.000
7:76397732:C:G	W218C	1.000
7:76390174:T:A	D538V	0.999
7:76390281:C:A	W502C	0.999
7:76390281:C:G	W502C	0.999
7:76390294:C:G	C498S	0.999
7:76390294:C:T	C498Y	0.999
7:76390295:A:T	C498S	0.999
7:76393621:A:G	W373R	0.999
7:76393621:A:T	W373R	0.999
7:76397625:T:A	D254V	0.999
7:76397745:C:G	C214S	0.999
7:76397745:C:T	C214Y	0.999
7:76397746:A:T	C214S	0.999
7:76400500:C:A	W87C	0.999
7:76400500:C:G	W87C	0.999
7:76390088:C:G	D567H	0.998
7:76390102:C:G	C562S	0.998
7:76390103:A:T	C562S	0.998
7:76390162:C:G	C542S	0.998
7:76390163:A:T	C542S	0.998
7:76390288:T:A	D500V	0.998
7:76390291:T:A	D499V	0.998
7:76390293:A:C	C498W	0.998
7:76390294:C:A	C498F	0.998
7:76390297:A:T	V497D	0.998
7:76390305:C:A	W494C	0.998
7:76390305:C:G	W494C	0.998

dbSNP variants (sampled 300 via entrez): RS1000358685 (7:76392335 G>A), RS1000457420 (7:76391717 A>G,T), RS1000614248 (7:76397660 G>A), RS1000692624 (7:76390686 G>A), RS1000827265 (7:76409872 T>A), RS1001060809 (7:76401868 T>C), RS1001176285 (7:76403049 A>G), RS1001479555 (7:76408460 T>C), RS1001718332 (7:76399094 C>A), RS1001726254 (7:76404561 G>A), RS1001760293 (7:76404796 G>A,C), RS1001852698 (7:76393210 A>G,T), RS1002064919 (7:76402839 G>A), RS1002097338 (7:76403289 C>T), RS1002148761 (7:76411362 C>G,T)

Disease associations

OMIM: gene MIM:607639 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010244_401	Triglyceride levels	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	3
bisphenol A	affects expression, decreases expression	2
TAK-243	increases sumoylation	1
perfluoroheptanesulfonic acid	affects expression	1
terbufos	increases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
tobacco tar	decreases expression	1
2-palmitoylglycerol	increases expression	1
entinostat	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Caffeine	increases expression	1
Catechin	affects cotreatment, increases expression	1
Fonofos	increases methylation	1
Hydrogen Peroxide	affects expression	1
Parathion	increases methylation	1
Rotenone	increases expression	1
Triclosan	increases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Zearalenone	decreases expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Copper Sulfate	decreases expression	1
Genistein	decreases expression	1

Clinical trials (associated diseases)

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