SLAMF9

Summary

SLAMF9 (SLAM family member 9, HGNC:18430) is a protein-coding gene on chromosome 1q23.2, encoding SLAM family member 9 (Q96A28). May play a role in the immune response.

This gene encodes a member of the signaling lymphocytic activation molecule family. The encoded protein is a cell surface molecule that consists of two extracellular immunoglobulin domains, a transmembrane domain and a short cytoplasmic tail that lacks the signal transduction motifs found in other family members. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 89886 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_033438

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18430
Approved symbol	SLAMF9
Name	SLAM family member 9
Location	1q23.2
Locus type	gene with protein product
Status	Approved
Aliases	CD2F-10, CD84-H1, SF2001
Ensembl gene	ENSG00000162723
Ensembl biotype	protein_coding
OMIM	608589
Entrez	89886

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000368092, ENST00000368093, ENST00000466773, ENST00000489098

RefSeq mRNA: 3 — MANE Select: NM_033438 NM_001146172, NM_001146173, NM_033438

CCDS: CCDS1191, CCDS53392

Canonical transcript exons

ENST00000368093 — 4 exons

Exon	Start	End
ENSE00001068009	159953309	159953653
ENSE00001446303	159954092	159954237
ENSE00003475412	159951492	159951866
ENSE00003675921	159952262	159952534

Expression profiles

Bgee: expression breadth ubiquitous, 112 present calls, max score 86.19.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0241 / max 53.8943, expressed in 251 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15453	0.8910	228
15452	0.1330	57

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.19	gold quality
secondary oocyte	CL:0000655	62.53	gold quality
amniotic fluid	UBERON:0000173	61.63	silver quality
right lobe of liver	UBERON:0001114	60.64	gold quality
nasal cavity epithelium	UBERON:0005384	59.98	gold quality
cerebellar vermis	UBERON:0004720	59.60	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	59.16	gold quality
thymus	UBERON:0002370	58.21	gold quality
oocyte	CL:0000023	57.78	gold quality
lateral globus pallidus	UBERON:0002476	57.37	gold quality
epithelium of nasopharynx	UBERON:0001951	57.00	gold quality
palpebral conjunctiva	UBERON:0001812	55.58	gold quality
liver	UBERON:0002107	54.79	gold quality
superficial temporal artery	UBERON:0001614	54.77	gold quality
medulla oblongata	UBERON:0001896	54.40	gold quality
substantia nigra pars reticulata	UBERON:0001966	54.27	gold quality
superior vestibular nucleus	UBERON:0007227	53.97	gold quality
trigeminal ganglion	UBERON:0001675	53.85	gold quality
dorsal plus ventral thalamus	UBERON:0001897	53.72	gold quality
inferior vagus X ganglion	UBERON:0005363	53.72	gold quality
subthalamic nucleus	UBERON:0001906	53.53	gold quality
lateral nuclear group of thalamus	UBERON:0002736	53.53	gold quality
pons	UBERON:0000988	53.38	gold quality
dorsal root ganglion	UBERON:0000044	53.29	gold quality
layer of synovial tissue	UBERON:0007616	53.24	gold quality
mammary duct	UBERON:0001765	53.21	gold quality
saphenous vein	UBERON:0007318	52.98	gold quality
pericardium	UBERON:0002407	52.84	gold quality
synovial joint	UBERON:0002217	52.64	gold quality
penis	UBERON:0000989	52.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting SLAMF9, 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-3934-3P	99.76	65.51	1351
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-331-3P	98.76	64.91	793
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-6810-3P	97.96	64.57	1023
HSA-MIR-4308	97.56	67.13	1385

Literature-anchored findings (GeneRIF, showing 2)

• SLAMF9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection. (PMID:31880316)
• The prognostic and immune significance of SLAMF9 in pan-cancer and validation of its role in colorectal cancer. (PMID:39095516)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:cabz01074946.1	ENSDARG00000090396
mus_musculus	Slamf9	ENSMUSG00000026548
rattus_norvegicus	Slamf9	ENSRNOG00000008045

Paralogs (9): SLAMF7 (ENSG00000026751), CD84 (ENSG00000066294), CD2 (ENSG00000116824), SLAMF1 (ENSG00000117090), CD48 (ENSG00000117091), CD244 (ENSG00000122223), LY9 (ENSG00000122224), SLAMF8 (ENSG00000158714), SLAMF6 (ENSG00000162739)

Protein

Protein identifiers

SLAM family member 9 — Q96A28 (reviewed: Q96A28)

Alternative names: CD2 family member 10, CD84 homolog 1

All UniProt accessions (1): Q96A28

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the immune response.

Subcellular location. Membrane.

Tissue specificity. Expression is predominantly restricted in hematopoietic tissues. Expressed in heart, spleen, liver, intestine, muscle and testis. Expressed in immune cells, including monocytes, dendritic, B- and T-cells. No expression was seen in peripheral blood leukocytes. Expressed in the leukocyte cell line THP-1.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96A28-1	1	yes
Q96A28-2	2

RefSeq proteins (3): NP_001139644, NP_001139645, NP_254273* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007110	Ig-like_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR015631	CD2/SLAM_rcpt	Family
IPR036179	Ig-like_dom_sf	Homologous_superfamily

UniProt features (16 total): sequence variant 4, splice variant 2, topological domain 2, domain 2, glycosylation site 2, signal peptide 1, chain 1, transmembrane region 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96A28-F1	81.83	0.54

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 (1): 156–200

Glycosylation sites (2): 99, 208

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, GOCC_CELL_SURFACE, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, FOSTER_TOLERANT_MACROPHAGE_DN, GOCC_SIDE_OF_MEMBRANE, MGGAAGTG_GABP_B, CHEN_METABOLIC_SYNDROM_NETWORK, GOCC_EXTERNAL_SIDE_OF_PLASMA_MEMBRANE, GOBP_LYMPHOCYTE_ACTIVATION, KATSANOU_ELAVL1_TARGETS_UP, FOSTER_KDM1A_TARGETS_UP, NRL_DN.V1_DN, GOBP_T_CELL_ACTIVATION, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN

GO Biological Process (2): immune response (GO:0006955), T cell activation (GO:0042110)

GO Molecular Function (0):

GO Cellular Component (3): external side of plasma membrane (GO:0009897), cell surface (GO:0009986), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
immune system process	1
response to stimulus	1
lymphocyte activation	1
plasma membrane	1
cell surface	1
side of membrane	1

Protein interactions and networks

STRING

818 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLAMF9	CD2	P06729	740
SLAMF9	SLAMF8	Q9P0V8	728
SLAMF9	SH2D1B	O14796	541
SLAMF9	CD244	Q9BZW8	541
SLAMF9	CD48	P09326	511
SLAMF9	SH2D1A	O60880	480
SLAMF9	BPI	P17213	471
SLAMF9	CD58	P19256	460
SLAMF9	SEPTIN12	Q8IYM1	448
SLAMF9	SLAMF1	Q13291	445
SLAMF9	ARHGAP30	Q7Z6I6	367
SLAMF9	LPP	Q93052	353
SLAMF9	PDCD6IP	Q8WUM4	352
SLAMF9	AEBP2	Q6ZN18	351
SLAMF9	TM4SF19	Q96DZ7	321

IntAct

5 interactions, top by confidence:

A	B	Type	Score
SLAMF9	BPI	psi-mi:“MI:0915”(physical association)	0.400
SLAMF9	IGSF10	psi-mi:“MI:0915”(physical association)	0.400
INSYN1	CCDC85C	psi-mi:“MI:0914”(association)	0.350
SLAMF9	CAND2	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): CAND2 (Affinity Capture-MS), SLAMF9 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS)

ESM2 similar proteins: A2A7V7, A2TGX5, A5D7B2, G3X8R9, O88875, O95944, P0DMS9, P11912, P12318, P15530, P16410, P22273, P31785, P31994, P31995, P34902, P40259, P50283, Q02242, Q1ERP8, Q2LA85, Q2YFS1, Q2YFS2, Q2YFS3, Q3LRV9, Q3U497, Q566E6, Q5T2D2, Q60513, Q6SJQ0, Q6SJQ5, Q6SJQ7, Q6TYI6, Q6UXG3, Q6UXN2, Q7TSN2, Q86YW5, Q8K558, Q8SPV8, Q8TDQ1

Diamond homologs: Q01965, Q18PI6, Q8BHK6, Q96A28, Q96DU3, Q9D780, Q9HBG7, Q9NQ25, Q9UIB8, Q9ET39, P42071, Q3KPI0, Q4VAH7, Q9P0V8, A4FUY1, Q14CZ8, Q640R3, Q13291

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	7
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

528 predictions. Top by Δscore:

Variant	Effect	Δscore
1:159953327:A:AC	donor_gain	1.0000
1:159953328:C:CC	donor_gain	1.0000
1:159953328:CTG:C	donor_gain	1.0000
1:159953443:A:AC	donor_gain	1.0000
1:159953444:C:CC	donor_gain	1.0000
1:159951872:G:GC	acceptor_gain	0.9900
1:159953307:A:AC	donor_gain	0.9900
1:159953308:C:CC	donor_gain	0.9900
1:159953444:CTTGG:C	donor_gain	0.9900
1:159954062:T:A	donor_gain	0.9900
1:159954090:AC:A	donor_gain	0.9900
1:159954090:ACCCT:A	donor_gain	0.9900
1:159954091:CC:C	donor_gain	0.9900
1:159954091:CCCTC:C	donor_gain	0.9900
1:159951866:TC:T	acceptor_loss	0.9800
1:159951867:C:CC	acceptor_gain	0.9800
1:159951867:CTGG:C	acceptor_loss	0.9800
1:159951872:G:C	acceptor_gain	0.9800
1:159951863:GGAT:G	acceptor_gain	0.9700
1:159953424:G:C	donor_gain	0.9700
1:159953447:GGC:G	donor_gain	0.9700
1:159953656:A:C	acceptor_gain	0.9700
1:159954084:TCAC:T	donor_loss	0.9700
1:159954085:CACT:C	donor_loss	0.9700
1:159954086:ACTC:A	donor_loss	0.9700
1:159954087:CTCA:C	donor_loss	0.9700
1:159954088:T:TA	donor_loss	0.9700
1:159954089:C:CC	donor_loss	0.9700
1:159953498:T:A	donor_gain	0.9600
1:159953650:CTGC:C	acceptor_gain	0.9600

AlphaMissense

1903 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:159953537:A:G	W55R	0.766
1:159953537:A:T	W55R	0.766
1:159953535:C:A	W55C	0.757
1:159953535:C:G	W55C	0.757
1:159952419:C:A	W169C	0.698
1:159952419:C:G	W169C	0.698
1:159953378:A:C	Y108D	0.685
1:159952421:A:G	W169R	0.654
1:159952421:A:T	W169R	0.654
1:159953436:G:C	F88L	0.627
1:159953436:G:T	F88L	0.627
1:159953438:A:G	F88L	0.627
1:159952269:G:C	F219L	0.604
1:159952269:G:T	F219L	0.604
1:159952271:A:G	F219L	0.604
1:159952314:G:C	N204K	0.582
1:159952314:G:T	N204K	0.582
1:159953534:A:G	S56P	0.579
1:159952305:G:C	S207R	0.564
1:159952305:G:T	S207R	0.564
1:159952307:T:G	S207R	0.564

dbSNP variants (sampled 300 via entrez): RS1000112455 (1:159959215 A>C), RS1000185291 (1:159956047 C>T), RS1000303860 (1:159957499 C>G,T), RS1000322597 (1:159951494 G>A), RS1000359271 (1:159961602 A>C), RS1000367678 (1:159983616 G>C), RS1000474346 (1:159954020 C>T), RS1000479770 (1:159967669 G>A), RS1000521208 (1:159954459 C>A,G,T), RS1000709505 (1:159981199 A>G), RS1000774280 (1:159961794 T>C), RS1000806497 (1:159966331 T>A), RS1000906109 (1:159968865 A>T), RS1000991247 (1:159971983 C>T), RS1001031215 (1:159976240 T>C)

Disease associations

OMIM: gene MIM:608589 | 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
GCST008103_100	Bipolar disorder	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
beta-lapachone	increases expression	1
CGP 52608	affects binding, increases reaction	1
NSC 689534	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Estradiol	affects cotreatment, increases expression	1
Mustard Gas	increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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