SLA2

gene
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Also known as FLJ21992SLAP-2

Summary

SLA2 (Src like adaptor 2, HGNC:17329) is a protein-coding gene on chromosome 20q11.23, encoding Src-like-adapter 2 (Q9H6Q3). Adapter protein, which negatively regulates T-cell receptor (TCR) signaling.

This gene encodes a member of the SLAP family of adapter proteins. The encoded protein may play an important receptor-proximal role in downregulating T and B cell-mediated responses and inhibits antigen receptor-induced calcium mobilization. This protein interacts with Cas-Br-M (murine) ecotropic retroviral transforming sequence c. Two transcript variants encoding distinct isoforms have been identified for this gene.

Source: NCBI Gene 84174 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 49 total
  • MANE Select transcript: NM_032214

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17329
Approved symbolSLA2
NameSrc like adaptor 2
Location20q11.23
Locus typegene with protein product
StatusApproved
AliasesFLJ21992, SLAP-2
Ensembl geneENSG00000101082
Ensembl biotypeprotein_coding
OMIM606577
Entrez84174

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000262866, ENST00000360672, ENST00000876805, ENST00000876806, ENST00000948638, ENST00000948639

RefSeq mRNA: 2 — MANE Select: NM_032214 NM_032214, NM_175077

CCDS: CCDS13282, CCDS13283

Canonical transcript exons

ENST00000262866 — 8 exons

ExonStartEnd
ENSE000006617753663259536632698
ENSE000006617763661522536615374
ENSE000006617773661430536614437
ENSE000008004243663354336633629
ENSE000008004253663449036634589
ENSE000012901933664583736646196
ENSE000013883583664124536641378
ENSE000018942823661231836613986

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 91.62.

FANTOM5 (CAGE): breadth broad, TPM avg 5.8716 / max 260.4362, expressed in 246 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1871275.8716246

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233691.62gold quality
granulocyteCL:000009488.99gold quality
leukocyteCL:000073888.57gold quality
monocyteCL:000057688.50gold quality
bloodUBERON:000017887.64gold quality
ileal mucosaUBERON:000033182.55silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047377.95gold quality
lymph nodeUBERON:000002977.67gold quality
oviduct epitheliumUBERON:000480476.79gold quality
spleenUBERON:000210675.04gold quality
vermiform appendixUBERON:000115474.93gold quality
superficial temporal arteryUBERON:000161474.66silver quality
oocyteCL:000002373.80silver quality
bone marrow cellCL:000209273.77gold quality
bone marrowUBERON:000237173.62gold quality
nasal cavity epitheliumUBERON:000538471.98gold quality
amniotic fluidUBERON:000017371.88gold quality
secondary oocyteCL:000065570.23silver quality
caecumUBERON:000115370.08gold quality
right lungUBERON:000216769.84gold quality
thymusUBERON:000237069.55gold quality
colonic epitheliumUBERON:000039769.10gold quality
gall bladderUBERON:000211068.26gold quality
cardiac muscle of right atriumUBERON:000337968.00gold quality
left ventricle myocardiumUBERON:000656667.69gold quality
tibialis anteriorUBERON:000138566.84silver quality
upper lobe of left lungUBERON:000895266.50gold quality
upper lobe of lungUBERON:000894865.97gold quality
tonsilUBERON:000237265.89gold quality
nasal cavity mucosaUBERON:000182665.82gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-MTAB-6678yes29.37
E-CURD-122yes24.57
E-CURD-88yes20.29
E-ANND-3yes8.07
E-MTAB-9801yes5.92

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
CD69Unknown

miRNA regulators (miRDB)

71 targeting SLA2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4283100.0066.422097
HSA-MIR-3646100.0073.565283
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-185-3P99.9567.011743
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-449299.8768.253611
HSA-MIR-1211999.8768.351653
HSA-MIR-469899.8471.414303
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-430699.7270.503630
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-320299.6667.702737
HSA-MIR-182799.6368.573265
HSA-MIR-3682-3P99.5867.63865
HSA-MIR-76299.5866.611994
HSA-MIR-4762-5P99.5768.541424
HSA-MIR-6833-5P99.5068.931161

Literature-anchored findings (GeneRIF, showing 5)

  • negatively regulates T cell receptor signaling (PMID:11891219)
  • The human SLAP-2 gene is located on chromosome 20q, and the SLAP-2 coding region consists of seven exons, a unique cDNA encoding an alternatively spliced SLAP-2 isoform has been identified (PMID:12527895)
  • In platelets, SLAP-2 may have function as a negative regulator of GPVI-mediated signaling by interacting with c-Cbl. (PMID:20828795)
  • SLAP2 SH3 and SH2 domains are separated by a short SH3-SH2 connector sequence. (PMID:24018043)
  • SLAP2 Adaptor Binding Disrupts c-CBL Autoinhibition to Activate Ubiquitin Ligase Function. (PMID:33617900)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriosla2bENSDARG00000020788
danio_reriosla2aENSDARG00000099887
mus_musculusSla2ENSMUSG00000027636
rattus_norvegicusSla2ENSRNOG00000020337
drosophila_melanogasterdockFBGN0010583
caenorhabditis_elegansWBGENE00006410

Paralogs (9): DAPP1 (ENSG00000070190), NCK2 (ENSG00000071051), GRAP2 (ENSG00000100351), GRAP (ENSG00000154016), SLA (ENSG00000155926), NCK1 (ENSG00000158092), GRB2 (ENSG00000177885), GRAPL (ENSG00000189152), SH2D5 (ENSG00000189410)

Protein

Protein identifiers

Src-like-adapter 2Q9H6Q3 (reviewed: Q9H6Q3)

Alternative names: Modulator of antigen receptor signaling, Src-like adapter protein 2

All UniProt accessions (1): Q9H6Q3

UniProt curated annotations — full annotation on UniProt →

Function. Adapter protein, which negatively regulates T-cell receptor (TCR) signaling. Inhibits T-cell antigen-receptor induced activation of nuclear factor of activated T-cells. May act by linking signaling proteins such as ZAP70 with CBL, leading to a CBL dependent degradation of signaling proteins.

Subunit / interactions. Interacts (via SH2 domain) with ZAP70 (phosphorylated) and CD3Z (phosphorylated). Interacts (via SH2 domain) with CSF1R (phosphorylated). Interacts (via its C-terminal domain) with CBL (phosphorylated).

Subcellular location. Cytoplasm Cell membrane. Cytoplasmic vesicle Cytoplasm.

Tissue specificity. Predominantly expressed in immune system, with highest levels in peripheral blood leukocytes. Expressed in spleen, thymus and lymph nodes. Expressed in T-cells as well as in monocytes, and at low level in B-cells. Also detected in placenta, prostate, skin, retina and colon.

Post-translational modifications. Phosphorylated by CSF1R.

Domain organisation. The loss of the C-terminal domain partially abolishes the inhibitory function, but can be partially compensated by higher level of protein expression.

Miscellaneous. Produced by alternative initiation at Met-28 of isoform 1. Produced by alternative initiation at Met-28 of isoform 2.

Isoforms (4)

UniProt IDNamesCanonical?
Q9H6Q3-11, p28yes
Q9H6Q3-22, p23, SLAP-2-v, MARS-v
Q9H6Q3-33, p25
Q9H6Q3-44, p20

RefSeq proteins (2): NP_115590, NP_778252 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000980SH2Domain
IPR001452SH3_domainDomain
IPR035052SLAP_SH2Domain
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR036860SH2_dom_sfHomologous_superfamily
IPR043539Grb2-likeFamily

Pfam: PF00017, PF00018

UniProt features (30 total): strand 12, splice variant 3, helix 3, turn 2, domain 2, region of interest 2, initiator methionine 1, chain 1, sequence variant 1, mutagenesis site 1, compositionally biased region 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4M4ZX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H6Q3-F176.520.37

Functional residue map

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

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (1):

PositionPhenotype
2abolishes localization to membranes.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-9706369Negative regulation of FLT3
R-HSA-1280215Cytokine Signaling in Immune system
R-HSA-168256Immune System
R-HSA-9607240FLT3 Signaling

MSigDB gene sets: 134 (showing top): GOBP_REGULATION_OF_T_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_REGULATION_OF_CALCIUM_MEDIATED_SIGNALING, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, RACCACAR_AML_Q6, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_B_CELL_MEDIATED_IMMUNITY, GOBP_NEGATIVE_REGULATION_OF_T_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, TGCTGAY_UNKNOWN, GOBP_ADAPTIVE_IMMUNE_RESPONSE, GOBP_T_CELL_RECEPTOR_SIGNALING_PATHWAY

GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), B cell mediated immunity (GO:0019724), T cell activation (GO:0042110), regulation of immune response (GO:0050776), negative regulation of calcium-mediated signaling (GO:0050849), antigen receptor-mediated signaling pathway (GO:0050851), negative regulation of T cell receptor signaling pathway (GO:0050860)

GO Molecular Function (2): signaling adaptor activity (GO:0035591), protein binding (GO:0005515)

GO Cellular Component (10): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), late endosome (GO:0005770), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), endosome membrane (GO:0010008), endomembrane system (GO:0012505), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
FLT3 Signaling1
Immune System1
Cytokine Signaling in Immune system1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
cytoplasm3
endosome2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
lymphocyte mediated immunity1
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains1
lymphocyte activation1
regulation of immune system process1
immune response1
regulation of response to stimulus1
calcium-mediated signaling1
regulation of calcium-mediated signaling1
negative regulation of intracellular signal transduction1
immune response-activating cell surface receptor signaling pathway1
T cell receptor signaling pathway1
regulation of T cell receptor signaling pathway1
negative regulation of antigen receptor-mediated signaling pathway1
protein-macromolecule adaptor activity1
binding1
nuclear lumen1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1
membrane1
cell periphery1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
vacuole1
plasma membrane1
intracellular vesicle1

Protein interactions and networks

STRING

1292 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLA2HIP1RO75146951
SLA2TLN2Q9Y4G6786
SLA2TLN1Q9Y490784
SLA2SLMAPQ14BN4777
SLA2HTTP42858736
SLA2CLTCQ00610734
SLA2SNAP91O60641703
SLA2NLRP2Q9NX02669
SLA2SLC29A1Q99808636
SLA2CBLP22681623
SLA2ZNF461Q8TAF7601
SLA2EPN3Q9H201596
SLA2EPN2O95208583
SLA2CLTCL1P53675580
SLA2FCHO1O14526574

IntAct

26 interactions, top by confidence:

ABTypeScore
PRKAA2SLA2psi-mi:“MI:0915”(physical association)0.560
UBASH3ASLA2psi-mi:“MI:0915”(physical association)0.560
EGFRSLA2psi-mi:“MI:0915”(physical association)0.550
SLA2EGFRpsi-mi:“MI:0915”(physical association)0.550
MAP1LC3ASLA2psi-mi:“MI:0407”(direct interaction)0.440
SLA2ERBB2psi-mi:“MI:0407”(direct interaction)0.440
SLA2GAB1psi-mi:“MI:0407”(direct interaction)0.440
SLA2KITpsi-mi:“MI:0407”(direct interaction)0.440
SLA2METpsi-mi:“MI:0407”(direct interaction)0.440
ALKSLA2psi-mi:“MI:0915”(physical association)0.370
ALBCNOT1psi-mi:“MI:0914”(association)0.350
SLA2RPSA2psi-mi:“MI:0914”(association)0.350
PRKAA2SLA2psi-mi:“MI:0915”(physical association)0.000
UBASH3ASLA2psi-mi:“MI:0915”(physical association)0.000

BioGRID (39): SLA2 (Two-hybrid), SLA2 (PCA), UBASH3A (Two-hybrid), PRKAA2 (Two-hybrid), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), SLA2 (Reconstituted Complex), CD247 (Affinity Capture-Western), ZAP70 (Affinity Capture-Western), CBL (Affinity Capture-Western), SLA2 (Reconstituted Complex)

ESM2 similar proteins: A1A4I4, A1A5B6, A1DZY4, A4D2P6, A5D7J5, O35141, O35929, O62683, O75628, O88667, O88910, O88954, P04629, P0C7J6, P35739, P55040, P55041, P55042, P55043, P70268, Q13368, Q16512, Q3MII6, Q3UFB7, Q5E9J3, Q5EBH1, Q5R541, Q60806, Q63433, Q6IMA7, Q6IMB1, Q6P5Z2, Q7L0Q8, Q864R5, Q8IYK8, Q8K045, Q8R4L0, Q8VEL9, Q8VHP8, Q8WWW0

Diamond homologs: A0A8I3NFE2, A0JNB0, A1Y2K1, A6QLK6, B2RZ59, D7PF45, F1N9Y5, G5ECJ6, O14796, O15357, O35324, O45539, O60880, O88890, P00519, P00520, P00521, P00522, P00523, P00524, P00525, P00526, P05480, P06239, P06240, P06241, P08103, P08631, P10447, P10936, P12931, P13115, P13116, P14084, P14085, P15054, P16277, P25020, P29349, P31693

SIGNOR signaling

1 interactions.

AEffectBMechanism
SLA2“down-regulates activity”FLT3binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 12 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Constitutive Signaling by Aberrant PI3K in Cancer563.4×1e-06
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling548.4×3e-06
PIP3 activates AKT signaling533.4×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1328 predictions. Top by Δscore:

VariantEffectΔscore
20:36613985:AGC:Aacceptor_loss1.0000
20:36613986:GCTG:Gacceptor_loss1.0000
20:36613987:C:CCacceptor_gain1.0000
20:36632591:TCACC:Tdonor_loss1.0000
20:36632592:CACCT:Cdonor_loss1.0000
20:36632593:A:ACdonor_gain1.0000
20:36632594:C:CAdonor_loss1.0000
20:36632594:C:CCdonor_gain1.0000
20:36632594:CCT:Cdonor_gain1.0000
20:36632594:CCTCT:Cdonor_gain1.0000
20:36632695:CCAC:Cacceptor_gain1.0000
20:36632696:CAC:Cacceptor_gain1.0000
20:36632696:CACC:Cacceptor_gain1.0000
20:36632699:C:Tacceptor_loss1.0000
20:36632700:T:Gacceptor_loss1.0000
20:36632703:C:CTacceptor_gain1.0000
20:36632708:C:CTacceptor_gain1.0000
20:36632709:G:Tacceptor_gain1.0000
20:36633541:A:ACdonor_gain1.0000
20:36633542:C:CCdonor_gain1.0000
20:36633627:TCC:Tacceptor_gain1.0000
20:36633628:CC:Cacceptor_gain1.0000
20:36633628:CCC:Cacceptor_gain1.0000
20:36633629:CC:Cacceptor_gain1.0000
20:36633630:CTG:Cacceptor_loss1.0000
20:36633631:T:Aacceptor_loss1.0000
20:36634488:A:ACdonor_gain1.0000
20:36634489:C:CCdonor_gain1.0000
20:36634489:CT:Cdonor_gain1.0000
20:36613843:C:Adonor_gain0.9900

AlphaMissense

1668 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:36632623:G:CF118L0.997
20:36632623:G:TF118L0.997
20:36632625:A:GF118L0.997
20:36615308:A:GI150T0.995
20:36615259:G:CF166L0.993
20:36615259:G:TF166L0.993
20:36615261:A:GF166L0.993
20:36615356:A:TV134D0.992
20:36632618:A:TI120N0.992
20:36615308:A:CI150S0.991
20:36632621:A:GL119P0.990
20:36632667:C:GA104P0.990
20:36632697:A:GW94R0.990
20:36632697:A:TW94R0.990
20:36615242:A:GL172P0.989
20:36615308:A:TI150N0.989
20:36632615:C:GR121P0.989
20:36615362:A:GL132P0.988
20:36614410:A:TL187H0.987
20:36632624:A:GF118S0.986
20:36615360:A:GS133P0.984
20:36615278:A:TI160N0.982
20:36615316:G:CH147Q0.982
20:36615316:G:TH147Q0.982
20:36615318:G:CH147D0.982
20:36632657:A:GL107P0.982
20:36632618:A:CI120S0.980
20:36632618:A:GI120T0.980
20:36632654:A:GL108P0.980
20:36615260:A:GF166S0.979

dbSNP variants (sampled 300 via entrez): RS1000035800 (20:36632176 T>C), RS1000107951 (20:36646966 T>A), RS1000234798 (20:36616039 A>G), RS1000261678 (20:36615044 C>T), RS1000295455 (20:36628700 C>T), RS1000480803 (20:36648001 C>T), RS1000718446 (20:36635047 G>A), RS1000788125 (20:36628149 C>G), RS1000795194 (20:36635277 C>G,T), RS1000811777 (20:36635259 A>G), RS1000863554 (20:36616254 A>G), RS1000888147 (20:36642206 G>C), RS1000948205 (20:36628461 A>T), RS1001140349 (20:36642362 C>A), RS1001197322 (20:36621198 C>T)

Disease associations

OMIM: gene MIM:606577 | 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

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression2
aristolochic acid Iincreases expression1
OTX015decreases expression1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
Arsenic Trioxideincreases expression1
Benzo(a)pyreneaffects methylation1
Caffeineincreases phosphorylation1
Calcitriolincreases expression, affects cotreatment1
Mercuric Chlorideaffects cotreatment, increases expression1
Nickelincreases expression1
Testosteroneincreases expression, affects cotreatment1
Urethanedecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1

Clinical trials (associated diseases)

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

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