SSC5D

Summary

SSC5D (scavenger receptor cysteine rich family member with 5 domains, HGNC:26641) is a protein-coding gene on chromosome 19q13.42, encoding Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D (A1L4H1). Binds to extracellular matrix proteins.

Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in defense response; detection of bacterial lipoprotein; and negative regulation of interleukin-8 production. Predicted to act upstream of or within regulation of interleukin-8 production. Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular matrix and extracellular space.

Source: NCBI Gene 284297 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 398 total
• MANE Select transcript: NM_001144950

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26641
Approved symbol	SSC5D
Name	scavenger receptor cysteine rich family member with 5 domains
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35258, S5D-SRCRB
Ensembl gene	ENSG00000179954
Ensembl biotype	protein_coding
OMIM	618194
Entrez	284297

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000389623, ENST00000587166, ENST00000588254, ENST00000589020, ENST00000594321

RefSeq mRNA: 2 — MANE Select: NM_001144950 NM_001144950, NM_001195267

CCDS: CCDS46196, CCDS59424

Canonical transcript exons

ENST00000389623 — 14 exons

Exon	Start	End
ENSE00001506391	55517224	55519099
ENSE00001506395	55513011	55513172
ENSE00001506396	55501034	55501201
ENSE00001506397	55500490	55500804
ENSE00001506399	55499816	55500412
ENSE00001506400	55497880	55498197
ENSE00001506402	55493595	55493912
ENSE00001506403	55490772	55491080
ENSE00001506406	55489354	55489662
ENSE00001506407	55489006	55489032
ENSE00003045826	55494610	55494783
ENSE00003582060	55490298	55490408
ENSE00003604914	55489882	55489995
ENSE00003847917	55488436	55488614

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 98.58.

FANTOM5 (CAGE): breadth broad, TPM avg 5.9528 / max 141.5929, expressed in 862 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177624	3.8773	789
177625	1.5466	476
177626	0.5288	276

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	98.58	gold quality
stromal cell of endometrium	CL:0002255	96.33	gold quality
kidney epithelium	UBERON:0004819	94.58	gold quality
vena cava	UBERON:0004087	94.11	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.31	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	90.92	silver quality
saphenous vein	UBERON:0007318	90.22	gold quality
buccal mucosa cell	CL:0002336	89.30	silver quality
pericardium	UBERON:0002407	89.14	gold quality
body of uterus	UBERON:0009853	88.95	gold quality
parotid gland	UBERON:0001831	88.62	silver quality
layer of synovial tissue	UBERON:0007616	88.60	gold quality
muscle layer of sigmoid colon	UBERON:0035805	88.39	gold quality
pancreatic ductal cell	CL:0002079	88.30	silver quality
cardia of stomach	UBERON:0001162	87.78	silver quality
synovial joint	UBERON:0002217	87.69	gold quality
nipple	UBERON:0002030	87.54	gold quality
left uterine tube	UBERON:0001303	87.53	gold quality
myometrium	UBERON:0001296	87.35	gold quality
lateral globus pallidus	UBERON:0002476	87.24	silver quality
smooth muscle tissue	UBERON:0001135	87.02	gold quality
decidua	UBERON:0002450	86.90	gold quality
body of tongue	UBERON:0011876	86.18	silver quality
pylorus	UBERON:0001166	86.08	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.57	gold quality
urethra	UBERON:0000057	85.55	gold quality
pharyngeal mucosa	UBERON:0000355	85.02	silver quality
pons	UBERON:0000988	85.02	gold quality
trachea	UBERON:0003126	84.72	silver quality
substantia nigra pars reticulata	UBERON:0001966	84.57	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SSC5D, 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-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-1228-3P	99.00	66.53	857
HSA-MIR-4749-3P	96.40	66.24	798

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-14d8.20	ENSDARG00000045837
danio_rerio	si:ch211-150o23.3	ENSDARG00000078502
mus_musculus	Ssc5d	ENSMUSG00000035279
rattus_norvegicus	Ssc5d	ENSRNOG00000016687
drosophila_melanogaster	Loxl2	FBGN0034660

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), DMBT1 (ENSG00000187908), SCART1 (ENSG00000214279)

Protein

Protein identifiers

Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D — A1L4H1 (reviewed: A1L4H1)

Alternative names: Soluble scavenger protein with 5 SRCR domains

All UniProt accessions (3): A1L4H1, K7EPL3, M0QZ17

UniProt curated annotations — full annotation on UniProt →

Function. Binds to extracellular matrix proteins. Binds to pathogen-associated molecular patterns (PAMPs) present on the cell walls of Gram-positive and Gram-negative bacteria and fungi, behaving as a pattern recognition receptor (PRR). Induces bacterial and fungal aggregation and subsequent inhibition of PAMP-induced cytokine release. Does not possess intrinsic bactericidal activity. May play a role in the innate defense and homeostasis of certain epithelial surfaces.

Subunit / interactions. Interacts with LGALS1 and laminin.

Subcellular location. Secreted. Cytoplasm.

Tissue specificity. Highly expressed in monocytes/macrophages and T-lymphocytes. Highly expressed in placenta and spleen, and also detected at lower levels in colon, and more weakly in lung, heart and kidney.

Isoforms (2)

UniProt ID	Names	Canonical?
A1L4H1-1	1	yes
A1L4H1-2	2

RefSeq proteins (2): NP_001138422, NP_001182196 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001190	SRCR	Domain
IPR036772	SRCR-like_dom_sf	Homologous_superfamily

Pfam: PF00530

UniProt features (54 total): compositionally biased region 19, disulfide bond 15, region of interest 5, domain 5, glycosylation site 3, sequence conflict 3, splice variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1L4H1-F1	52.46	0.15

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 (15): 45–109, 58–119, 89–99, 223–287, 236–297, 267–277, 329–393, 342–403, 373–383, 492–557, 505–567, 537–547, 797–861, 810–871, 841–851

Glycosylation sites (3): 168, 376, 420

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-3000471	Scavenging by Class B Receptors
R-HSA-2173782	Binding and Uptake of Ligands by Scavenger Receptors
R-HSA-5653656	Vesicle-mediated transport

MSigDB gene sets: 79 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_DETECTION_OF_OTHER_ORGANISM, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_CYTOKINE_PRODUCTION, GOBP_DETECTION_OF_MOLECULE_OF_BACTERIAL_ORIGIN, GOBP_DEFENSE_RESPONSE_TO_GRAM_NEGATIVE_BACTERIUM, GOBP_NEGATIVE_REGULATION_OF_INTERLEUKIN_8_PRODUCTION, GOBP_DEFENSE_RESPONSE_TO_GRAM_POSITIVE_BACTERIUM, GOBP_DETECTION_OF_STIMULUS, GOBP_DEFENSE_RESPONSE_TO_BACTERIUM, GOBP_NEGATIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN, GOMF_EXTRACELLULAR_MATRIX_BINDING

GO Biological Process (9): defense response (GO:0006952), negative regulation of interleukin-8 production (GO:0032717), detection of bacterial lipoprotein (GO:0042494), innate immune response (GO:0045087), defense response to Gram-negative bacterium (GO:0050829), defense response to Gram-positive bacterium (GO:0050830), immune system process (GO:0002376), vesicle-mediated transport (GO:0016192), regulation of interleukin-8 production (GO:0032677)

GO Molecular Function (5): fibronectin binding (GO:0001968), scavenger receptor activity (GO:0005044), laminin binding (GO:0043236), extracellular matrix binding (GO:0050840), protein binding (GO:0005515)

GO Cellular Component (5): obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), membrane (GO:0016020), extracellular matrix (GO:0031012), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Binding and Uptake of Ligands by Scavenger Receptors	1
Vesicle-mediated transport	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
interleukin-8 production	2
defense response to bacterium	2
protein binding	2
binding	2
response to stress	1
negative regulation of cytokine production	1
regulation of interleukin-8 production	1
detection of bacterium	1
detection of molecule of bacterial origin	1
response to bacterial lipoprotein	1
immune response	1
defense response to symbiont	1
biological_process	1
transport	1
cellular process	1
regulation of cytokine production	1
cargo receptor activity	1
extracellular matrix binding	1
intracellular anatomical structure	1
external encapsulating structure	1

Protein interactions and networks

STRING

866 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSC5D	S4R460	S4R460	418
SSC5D	RAB7B	Q96AH8	359
SSC5D	GIMAP2	Q9UG22	354
SSC5D	SPDYE4	A6NLX3	352
SSC5D	TMPRSS5	Q9H3S3	350
SSC5D	SPDYC	Q5MJ68	328
SSC5D	ZNF524	Q96C55	320
SSC5D	VCF2	Q5XKR9	311
SSC5D	LDLRAD2	Q5SZI1	306
SSC5D	KRTAP9-2	Q9BYQ4	305
SSC5D	ZNF98	A6NK75	295
SSC5D	C6orf136	Q5SQH8	290
SSC5D	FRG2C	A6NGY1	290
SSC5D	COMTD1	Q86VU5	290
SSC5D	CCDC8	Q9H0W5	276

IntAct

73 interactions, top by confidence:

A	B	Type	Score
NECAB2	SSC5D	psi-mi:“MI:0915”(physical association)	0.720
NUP62	SSC5D	psi-mi:“MI:0915”(physical association)	0.720
SSC5D	MED21	psi-mi:“MI:0915”(physical association)	0.720
SSC5D	SEC23IP	psi-mi:“MI:0915”(physical association)	0.720
MED21	SSC5D	psi-mi:“MI:0915”(physical association)	0.720
SEC23IP	SSC5D	psi-mi:“MI:0915”(physical association)	0.720
SSC5D	NECAB2	psi-mi:“MI:0915”(physical association)	0.720
SSC5D	NUP62	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	SSC5D	psi-mi:“MI:0915”(physical association)	0.560
DTNBP1	SSC5D	psi-mi:“MI:0915”(physical association)	0.560
CEP170P1	SSC5D	psi-mi:“MI:0915”(physical association)	0.560
SSC5D	EXOC7	psi-mi:“MI:0915”(physical association)	0.560
SSC5D	TRAF1	psi-mi:“MI:0915”(physical association)	0.560
SSC5D	CEP170P1	psi-mi:“MI:0915”(physical association)	0.560
EXOC7	SSC5D	psi-mi:“MI:0915”(physical association)	0.560
SSC5D	DTNBP1	psi-mi:“MI:0915”(physical association)	0.560
SSC5D	PIN1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (34): SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), CEP170P1 (Two-hybrid), GCC2 (Affinity Capture-MS), SSC5D (Affinity Capture-MS), RRAS (Affinity Capture-MS), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (Two-hybrid), SSC5D (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	335
Likely benign	37
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1903 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55490296:A:AG	acceptor_gain	1.0000
19:55490297:G:GC	acceptor_gain	1.0000
19:55490297:GC:G	acceptor_gain	1.0000
19:55490297:GCC:G	acceptor_gain	1.0000
19:55490297:GCCC:G	acceptor_gain	1.0000
19:55490297:GCCCC:G	acceptor_gain	1.0000
19:55490405:CAAGG:C	donor_loss	1.0000
19:55490406:AAGG:A	donor_loss	1.0000
19:55490408:GGT:G	donor_loss	1.0000
19:55490409:G:GG	donor_gain	1.0000
19:55490409:GTAAG:G	donor_loss	1.0000
19:55490410:T:G	donor_loss	1.0000
19:55489658:CGCAG:C	donor_loss	0.9900
19:55489659:GCAGG:G	donor_loss	0.9900
19:55489660:CAGG:C	donor_loss	0.9900
19:55489661:AGGTG:A	donor_loss	0.9900
19:55489662:GGTGA:G	donor_loss	0.9900
19:55489663:G:C	donor_loss	0.9900
19:55489664:T:A	donor_loss	0.9900
19:55489877:C:A	acceptor_gain	0.9900
19:55489879:CAG:C	acceptor_loss	0.9900
19:55489881:G:GA	acceptor_loss	0.9900
19:55489992:CATGG:C	donor_loss	0.9900
19:55489994:TGGT:T	donor_loss	0.9900
19:55489995:GGTG:G	donor_loss	0.9900
19:55489996:G:GG	donor_gain	0.9900
19:55489996:GT:G	donor_loss	0.9900
19:55489997:T:A	donor_loss	0.9900
19:55490290:A:AG	acceptor_gain	0.9900
19:55490291:C:G	acceptor_gain	0.9900

AlphaMissense

10001 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55490866:G:C	W227C	1.000
19:55490866:G:T	W227C	1.000
19:55493698:G:C	W333C	1.000
19:55493698:G:T	W333C	1.000
19:55489448:G:C	W49C	0.999
19:55489448:G:T	W49C	0.999
19:55490842:G:C	W219C	0.999
19:55490842:G:T	W219C	0.999
19:55491031:G:C	W282C	0.999
19:55491031:G:T	W282C	0.999
19:55493685:G:A	C329Y	0.999
19:55493696:T:A	W333R	0.999
19:55493696:T:C	W333R	0.999
19:55489613:G:C	W104C	0.998
19:55489613:G:T	W104C	0.998
19:55490853:G:A	C223Y	0.998
19:55490864:T:A	W227R	0.998
19:55490864:T:C	W227R	0.998
19:55490892:G:A	C236Y	0.998
19:55490893:C:G	C236W	0.998
19:55490968:G:C	W261C	0.998
19:55490968:G:T	W261C	0.998
19:55491044:T:A	C287S	0.998
19:55491045:G:A	C287Y	0.998
19:55491045:G:C	C287S	0.998
19:55491076:C:G	C297W	0.998
19:55493674:G:C	W325C	0.998
19:55493674:G:T	W325C	0.998
19:55493816:T:A	C373S	0.998
19:55493816:T:C	C373R	0.998

dbSNP variants (sampled 300 via entrez): RS1000094188 (19:55489377 C>T), RS1000318490 (19:55488449 C>A,T), RS1000372843 (19:55499479 G>A,T), RS1000470245 (19:55492883 A>G), RS1000558073 (19:55508282 G>A), RS1000596477 (19:55508619 T>C), RS1000713416 (19:55514678 C>T), RS1000774188 (19:55488033 C>A), RS1000862518 (19:55491639 G>A), RS1000913074 (19:55503073 A>G), RS1000968632 (19:55498099 G>A,T), RS1000969837 (19:55497054 C>T), RS1001013698 (19:55507866 C>T), RS1001019901 (19:55502925 C>A,G), RS1001049348 (19:55488183 C>A,G)

Disease associations

OMIM: gene MIM:618194 | 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):

Study	Trait	p-value
GCST004744_3	Lung adenocarcinoma	4.000000e-06
GCST008163_458	Height	4.000000e-07

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
Tobacco Smoke Pollution	affects expression, decreases expression	2
daidzein	affects cotreatment, affects expression	1
daidzin	affects cotreatment, affects expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
genistin	affects expression, affects cotreatment	1
glycitein	affects cotreatment, affects expression	1
perfluoro-n-nonanoic acid	affects expression	1
glycitin	affects cotreatment, affects expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Calcitriol	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Latex	decreases expression	1
Lipopolysaccharides	increases expression, affects cotreatment, decreases expression, affects response to substance	1
Nickel	decreases expression	1
Oxygen	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Gold Compounds	increases expression	1
Cadmium Chloride	increases expression	1
Genistein	affects cotreatment, affects expression	1

Clinical trials (associated diseases)

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