SAMSN1

gene
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Also known as NASH1SASH2SH3D6BHACS1SLy2

Summary

SAMSN1 (SAM domain, SH3 domain and nuclear localization signals 1, HGNC:10528) is a protein-coding gene on chromosome 21q11.2, encoding SAM domain-containing protein SAMSN-1 (Q9NSI8). Negative regulator of B-cell activation.

SAMSN1 is a member of a novel gene family of putative adaptors and scaffold proteins containing SH3 and SAM (sterile alpha motif) domains (Claudio et al., 2001 [PubMed 11536050]).

Source: NCBI Gene 64092 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 63 total
  • Druggable target: yes
  • MANE Select transcript: NM_022136

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10528
Approved symbolSAMSN1
NameSAM domain, SH3 domain and nuclear localization signals 1
Location21q11.2
Locus typegene with protein product
StatusApproved
AliasesNASH1, SASH2, SH3D6B, HACS1, SLy2
Ensembl geneENSG00000155307
Ensembl biotypeprotein_coding
OMIM607978
Entrez64092

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000285670, ENST00000400562, ENST00000400564, ENST00000400566, ENST00000435732, ENST00000463807, ENST00000467280, ENST00000469393, ENST00000493640, ENST00000619120, ENST00000644288, ENST00000647101, ENST00000871911, ENST00000959353

RefSeq mRNA: 6 — MANE Select: NM_022136 NM_001256370, NM_001256579, NM_001286523, NM_001395857, NM_001395858, NM_022136

CCDS: CCDS42906, CCDS58786, CCDS74774, CCDS93082

Canonical transcript exons

ENST00000400566 — 8 exons

ExonStartEnd
ENSE000010202401451689214517041
ENSE000010202421451031014510461
ENSE000010202441450052914500735
ENSE000010202451451244414512573
ENSE000013088931452115014521221
ENSE000015435161454620514546315
ENSE000036058931449844214498592
ENSE000039038021448522814486114

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 96.04.

FANTOM5 (CAGE): breadth broad, TPM avg 58.9810 / max 5507.1735, expressed in 738 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
18976855.8122675
1897692.4507383
1897790.5246120
1897780.125358
1897800.053110
1897810.01515

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bone marrowUBERON:000237196.04gold quality
vermiform appendixUBERON:000115494.99gold quality
bone marrow cellCL:000209294.48gold quality
monocyteCL:000057694.11gold quality
mononuclear cellCL:000084294.09gold quality
leukocyteCL:000073893.89gold quality
right lungUBERON:000216793.20gold quality
bloodUBERON:000017893.17gold quality
spleenUBERON:000210691.87gold quality
lymph nodeUBERON:000002990.75gold quality
epithelium of nasopharynxUBERON:000195190.50gold quality
nasopharynxUBERON:000172890.48gold quality
trabecular bone tissueUBERON:000248389.53gold quality
gall bladderUBERON:000211089.36gold quality
granulocyteCL:000009488.58gold quality
caecumUBERON:000115388.43gold quality
superficial temporal arteryUBERON:000161488.43gold quality
upper lobe of left lungUBERON:000895288.35gold quality
lower lobe of lungUBERON:000894987.93gold quality
upper lobe of lungUBERON:000894887.85gold quality
periodontal ligamentUBERON:000826686.39gold quality
colonic epitheliumUBERON:000039786.25gold quality
rectumUBERON:000105286.22gold quality
omental fat padUBERON:001041485.97gold quality
peritoneumUBERON:000235885.89gold quality
lungUBERON:000204885.80gold quality
adipose tissue of abdominal regionUBERON:000780884.78gold quality
mucosa of sigmoid colonUBERON:000499383.75gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.12gold quality
small intestine Peyer’s patchUBERON:000345482.80gold quality

Single-cell (SCXA)

Detected in 26 experiment(s), a significant marker in 24.

ExperimentMarker?Max mean expression
E-ANND-2yes3151.99
E-GEOD-130148yes2293.20
E-MTAB-7381yes780.18
E-MTAB-8142yes90.85
E-HCAD-1yes68.03
E-CURD-88yes43.05
E-GEOD-135922yes42.78
E-GEOD-84465yes36.53
E-HCAD-35yes30.30
E-CURD-122yes27.22
E-CURD-46yes21.88
E-MTAB-8410yes18.24
E-HCAD-10yes15.66
E-CURD-112yes15.52
E-MTAB-9067yes12.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting SAMSN1, 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-5011-5P100.0083.465820
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3646100.0073.565283
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-366299.9973.825684
HSA-MIR-318599.9968.121959
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-570-3P99.9672.414910
HSA-MIR-590-3P99.9674.346478
HSA-LET-7C-3P99.9573.422862
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-314399.9371.963104
HSA-MIR-61399.9171.501710
HSA-MIR-990299.8969.152250
HSA-MIR-129-5P99.8870.263273
HSA-MIR-576-5P99.8470.462582
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-4645-3P99.7669.33993
HSA-MIR-442299.7272.072908
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-7159-5P99.5372.122472

Literature-anchored findings (GeneRIF, showing 8)

  • HACS1 is up-regulated by B cell activation signals and is a participant in B cell activation and differentiation. (PMID:15381729)
  • downregulation of SAMSN1 gene in human lung cancer. (PMID:18523997)
  • In the nucleus, SLy2 interacts with the SAP30/HDAC1 complex and regulates the activity of HDAC1. (PMID:20478393)
  • the immunoinhibitory roles of SLy2 in vivo and suggest that the physiological up-regulation of SLy2 observed upon B cell activation functions to counteract excessive B cell spreading. (PMID:21296879)
  • High expression of SAMSN1 is a significant risk factor for the progression free and overall survival of glioblastoma multiforme (PMID:24278465)
  • This is the first study to identify deletion of a key gene in the C57BL/KaLwRij mice that also displays reduced gene expression in patients with MM and is therefore likely to play an integral role in MM disease development. (PMID:25117979)
  • Suppression of SAMSN1 Expression is Associated with the Malignant Phenotype of Hepatocellular Carcinoma. (PMID:25805236)
  • HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain. (PMID:33188360)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosamsn1aENSDARG00000054543
danio_reriosamsn1bENSDARG00000078647
mus_musculusSamsn1ENSMUSG00000022876
rattus_norvegicusSamsn1ENSRNOG00000030930

Paralogs (2): SASH1 (ENSG00000111961), SASH3 (ENSG00000122122)

Protein

Protein identifiers

SAM domain-containing protein SAMSN-1Q9NSI8 (reviewed: Q9NSI8)

Alternative names: Hematopoietic adaptor containing SH3 and SAM domains 1, Nash1, SAM domain, SH3 domain and nuclear localization signals protein 1, SH3-SAM adaptor protein

All UniProt accessions (3): Q9NSI8, A0A2R8Y4K8, S6FRS6

UniProt curated annotations — full annotation on UniProt →

Function. Negative regulator of B-cell activation. Down-regulates cell proliferation (in vitro). Promotes RAC1-dependent membrane ruffle formation and reorganization of the actin cytoskeleton. Regulates cell spreading and cell polarization. Stimulates HDAC1 activity. Regulates LYN activity by modulating its tyrosine phosphorylation.

Subunit / interactions. Interacts with FASLG. Interacts with phosphotyrosine containing proteins. Interacts (via SH3 domain) with CTTN. Interacts (phosphorylated at Ser-23) with YWHAB, YWHAE, YWHAG, YWHAH, YWHAZ and SFN. Interacts directly with SAP30 and HDAC1. Identified in a complex with SAP30 and HDAC1.

Subcellular location. Nucleus. Cytoplasm. Cell projection. Ruffle.

Tissue specificity. Detected in peripheral blood B-cells (at protein level). Detected in spleen, liver and peripheral blood.

Induction. Up-regulated in peripheral blood B-cells by IL4, IL13 and by CD40 stimulation.

Isoforms (3)

UniProt IDNamesCanonical?
Q9NSI8-11yes
Q9NSI8-22, b
Q9NSI8-33

RefSeq proteins (5): NP_001243299, NP_001273452, NP_001382786, NP_001382787, NP_071419* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001452SH3_domainDomain
IPR001660SAMDomain
IPR013761SAM/pointed_sfHomologous_superfamily
IPR021090SPIDERDomain
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR037623SAMSN1_SAMDomain
IPR051725SAM-SH3_domain_proteinFamily

Pfam: PF07647, PF07653, PF12485

UniProt features (29 total): modified residue 7, strand 5, sequence conflict 3, region of interest 3, compositionally biased region 3, domain 2, splice variant 2, chain 1, sequence variant 1, helix 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6UZJSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NSI8-F164.110.27

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 (7): 23, 34, 74, 76, 90, 119, 160

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 377 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_PEPTIDYL_TYROSINE_PHOSPHORYLATION, WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_NEGATIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, MCLACHLAN_DENTAL_CARIES_UP, LU_IL4_SIGNALING, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_B_CELL_ACTIVATION, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_NEGATIVE_REGULATION_OF_B_CELL_ACTIVATION, GOCC_RUFFLE, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, NFKB_Q6, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS

GO Biological Process (4): negative regulation of adaptive immune response (GO:0002820), negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732), negative regulation of B cell activation (GO:0050869), regulation of intracellular signal transduction (GO:1902531)

GO Molecular Function (3): phosphotyrosine residue binding (GO:0001784), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (5): ruffle (GO:0001726), nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
adaptive immune response1
regulation of adaptive immune response1
negative regulation of immune response1
negative regulation of protein phosphorylation1
peptidyl-tyrosine phosphorylation1
regulation of peptidyl-tyrosine phosphorylation1
B cell activation1
regulation of B cell activation1
negative regulation of lymphocyte activation1
regulation of signal transduction1
intracellular signal transduction1
protein phosphorylated amino acid binding1
nucleic acid binding1
binding1
cell leading edge1
plasma membrane bounded cell projection1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1212 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SAMSN1CRKLP46109636
SAMSN1KIAA1143Q96AT1606
SAMSN1CRKP46108563
SAMSN1CRTAMO95727524
SAMSN1TMEM204Q9BSN7509
SAMSN1FCRL3Q96P31475
SAMSN1STAT6P42226463
SAMSN1DKKL1Q9UK85461
SAMSN1PRSS36Q5K4E3456
SAMSN1RBM11P57052450
SAMSN1KLF12Q9Y4X4450
SAMSN1CXCR3P49682446
SAMSN1PDCD1Q15116438
SAMSN1LILRB4Q8NHJ6435
SAMSN1DEF8Q6ZN54420

IntAct

13 interactions, top by confidence:

ABTypeScore
SAMSN1FASLGpsi-mi:“MI:0407”(direct interaction)0.440
AGGF1BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
DGCR8VWA8psi-mi:“MI:2364”(proximity)0.270
GPKOWESYT2psi-mi:“MI:2364”(proximity)0.270
ILF3ESYT2psi-mi:“MI:2364”(proximity)0.270
LIN28BMEX3Apsi-mi:“MI:2364”(proximity)0.270
RPS3ESYT2psi-mi:“MI:2364”(proximity)0.270
SBDSRPSA2psi-mi:“MI:2364”(proximity)0.270
YWHAGRPSA2psi-mi:“MI:2364”(proximity)0.270
DDX6RPSA2psi-mi:“MI:2364”(proximity)0.270
NPM1SBNO1psi-mi:“MI:2364”(proximity)0.270
SAMSN1psi-mi:“MI:0915”(physical association)0.000

BioGRID (21): SAMSN1 (Proximity Label-MS), SAMSN1 (Proximity Label-MS), SAMSN1 (Proximity Label-MS), SAMSN1 (Protein-peptide), SAMSN1 (Affinity Capture-RNA), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), SAMSN1 (Reconstituted Complex), YWHAG (Affinity Capture-Western), SAMSN1 (Affinity Capture-Western), SAP30 (Affinity Capture-Western)

ESM2 similar proteins: A4IIJ3, A8KBE0, B2RWW0, O35867, O94885, P57725, P59808, Q12923, Q13009, Q3UG20, Q3UMG5, Q3UVC0, Q5DTU0, Q5PQ89, Q5TB30, Q5VUJ6, Q60610, Q69ZW3, Q6AWC2, Q6ING4, Q6P2L6, Q6PF55, Q6VAB6, Q6ZMN7, Q803Q4, Q86W92, Q8BLB8, Q8BZ05, Q8C0D4, Q8C115, Q8C8U0, Q8IVE3, Q8IWW6, Q8IZD2, Q8K3X6, Q8N4X5, Q8NDI1, Q8R4H2, Q8TEW0, Q8WZ64

Diamond homologs: A0JN71, O75995, O94885, P57725, P59672, P59808, Q8K352, Q92625, Q9NSI8, Q9XYM0, Q5TGI4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2396 predictions. Top by Δscore:

VariantEffectΔscore
21:14486112:TAA:Tacceptor_gain1.0000
21:14486112:TAAC:Tacceptor_loss1.0000
21:14486114:AC:Aacceptor_loss1.0000
21:14486115:C:CCacceptor_gain1.0000
21:14486116:T:Aacceptor_loss1.0000
21:14498436:A:ACdonor_gain1.0000
21:14498437:C:CCdonor_gain1.0000
21:14498437:CTTA:Cdonor_gain1.0000
21:14498438:TTACT:Tdonor_loss1.0000
21:14498439:TA:Tdonor_loss1.0000
21:14498440:A:ACdonor_gain1.0000
21:14498440:ACTT:Adonor_loss1.0000
21:14498440:ACTTT:Adonor_gain1.0000
21:14498441:C:CTdonor_gain1.0000
21:14498441:CT:Cdonor_gain1.0000
21:14498441:CTT:Cdonor_gain1.0000
21:14498441:CTTT:Cdonor_gain1.0000
21:14498441:CTTTC:Cdonor_gain1.0000
21:14498444:T:Adonor_gain1.0000
21:14498588:TATTC:Tacceptor_gain1.0000
21:14498589:ATTC:Aacceptor_gain1.0000
21:14498590:TTC:Tacceptor_gain1.0000
21:14498591:TC:Tacceptor_gain1.0000
21:14498591:TCC:Tacceptor_loss1.0000
21:14498592:CC:Cacceptor_gain1.0000
21:14498593:C:CAacceptor_loss1.0000
21:14498593:C:CCacceptor_gain1.0000
21:14498593:C:Tacceptor_gain1.0000
21:14498595:G:Cacceptor_gain1.0000
21:14498595:G:GCacceptor_gain1.0000

AlphaMissense

2485 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:14500649:G:CF216L1.000
21:14500649:G:TF216L1.000
21:14500651:A:GF216L1.000
21:14500656:A:GF214S1.000
21:14500690:A:GW203R1.000
21:14500690:A:TW203R1.000
21:14500652:T:AK215N0.999
21:14500652:T:GK215N0.999
21:14500653:T:AK215I0.999
21:14500654:T:CK215E0.999
21:14500655:G:CF214L0.999
21:14500655:G:TF214L0.999
21:14500657:A:GF214L0.999
21:14500662:C:TG212E0.999
21:14500683:C:TG205E0.999
21:14500688:C:AW203C0.999
21:14500688:C:GW203C0.999
21:14500696:C:GG201R0.999
21:14500696:C:TG201R0.999
21:14510320:A:GL184P0.999
21:14510320:A:TL184H0.999
21:14510340:A:CS177R0.999
21:14510340:A:TS177R0.999
21:14510342:T:GS177R0.999
21:14510349:G:CF174L0.999
21:14510349:G:TF174L0.999
21:14510351:A:GF174L0.999
21:14510368:G:TA168D0.999
21:14498519:A:GL281P0.998
21:14500650:A:GF216S0.998

dbSNP variants (sampled 300 via entrez): RS1000004130 (21:14602796 A>G), RS1000039544 (21:14553935 G>T), RS1000041523 (21:14489399 C>T), RS1000107926 (21:14631206 G>A,T), RS1000120253 (21:14625888 G>A,C), RS1000128797 (21:14576854 G>A,C), RS1000131043 (21:14504782 C>T), RS1000135821 (21:14631447 C>CT), RS1000144655 (21:14561712 A>G), RS1000159947 (21:14521307 T>C), RS1000165207 (21:14591565 T>C), RS1000173197 (21:14536863 A>G), RS1000176177 (21:14597484 G>A), RS1000181893 (21:14521440 C>A,T), RS1000219373 (21:14621678 T>C)

Disease associations

OMIM: gene MIM:607978 | 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):

StudyTraitp-value
GCST002690_19Very long-chain saturated fatty acid levels (fatty acid 20:0)7.000000e-07
GCST004224_1Coronary atherosclerosis (increased number of diseased vessels) (traffic exposure interaction)2.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006796very long-chain saturated fatty acid measurement
EFO:0007908traffic air pollution measurement
EFO:0007938coronary atherosclerosis measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067306 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.19Kd6.486nMCHEMBL5653589
8.19ED506.486nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149340: Binding affinity to human SAMSN1 incubated for 45 mins by Kinobead based pull down assaykd0.0065uM

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, decreases methylation2
perfluorooctane sulfonic aciddecreases expression2
Air Pollutantsaffects expression, increases abundance, increases response to substance2
Benzo(a)pyreneincreases expression2
Estradiolaffects cotreatment, increases expression, decreases expression2
Nickelincreases expression2
Tretinoinincreases expression2
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
cupric chlorideincreases expression1
nickel sulfateincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
Air Pollutants, Occupationalincreases expression1
Vehicle Emissionsincreases abundance, increases response to substance1
Caffeineincreases phosphorylation1
Calcitrioldecreases expression1
Carbamazepineaffects expression1
Cisplatinincreases expression1
Demecolcineincreases expression1
Formaldehydeincreases expression1
Naledaffects expression1
Ozoneincreases abundance, affects expression1
Dronabinolincreases expression1
Triclosandecreases expression1
Valproic Acidaffects expression1
Vincristineincreases expression1
Zincincreases expression1
Isotretinoinincreases expression1
Aflatoxin B1decreases methylation1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652382BindingBinding affinity to human SAMSN1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.