SYAP1

gene
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Also known as FLJ14495PRO3113

Summary

SYAP1 (synapse associated protein 1, HGNC:16273) is a protein-coding gene on chromosome Xp22.2, encoding Synapse-associated protein 1 (Q96A49). Plays a role in adipocyte differentiation by promoting mTORC2-mediated phosphorylation of AKT1 at ‘Ser-473’ after growth factor stimulation.

Involved in several processes, including TORC2 signaling; cellular response to epidermal growth factor stimulus; and cellular response to peptide hormone stimulus. Located in several cellular components, including Golgi apparatus; cytoplasmic side of plasma membrane; and nucleoplasm.

Source: NCBI Gene 94056 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 110 total
  • MANE Select transcript: NM_032796

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16273
Approved symbolSYAP1
Namesynapse associated protein 1
LocationXp22.2
Locus typegene with protein product
StatusApproved
AliasesFLJ14495, PRO3113
Ensembl geneENSG00000169895
Ensembl biotypeprotein_coding
Entrez94056

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000380155, ENST00000495743, ENST00000896382, ENST00000896383, ENST00000896384, ENST00000896385, ENST00000896386, ENST00000896387, ENST00000896388, ENST00000939106, ENST00000939107, ENST00000968847

RefSeq mRNA: 1 — MANE Select: NM_032796 NM_032796

CCDS: CCDS14177

Canonical transcript exons

ENST00000380155 — 9 exons

ExonStartEnd
ENSE000011505851675716216757309
ENSE000011505901675666316756721
ENSE000011505941675494516755093
ENSE000011506031674370116743840
ENSE000011506081674171616741789
ENSE000011506131673616616736232
ENSE000014839091676023216765340
ENSE000014839851671961216719899
ENSE000036600431673522716735345

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 95.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 84.3031 / max 1967.1136, expressed in 1827 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
19563672.23371826
1956379.66141551
1956351.2690873
1956380.8197209
1956390.319365

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481995.69silver quality
calcaneal tendonUBERON:000370193.32gold quality
ileal mucosaUBERON:000033193.31gold quality
jejunal mucosaUBERON:000039993.29gold quality
tibialis anteriorUBERON:000138593.22silver quality
adrenal tissueUBERON:001830393.18gold quality
left ventricle myocardiumUBERON:000656692.69silver quality
upper arm skinUBERON:000426392.59gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.81gold quality
epithelium of nasopharynxUBERON:000195191.79gold quality
deltoidUBERON:000147691.64silver quality
bronchial epithelial cellCL:000232891.22gold quality
bronchusUBERON:000218590.98gold quality
jejunumUBERON:000211590.97gold quality
esophagus squamous epitheliumUBERON:000692090.93gold quality
nasal cavity epitheliumUBERON:000538490.81silver quality
myocardiumUBERON:000234990.47silver quality
deciduaUBERON:000245090.34gold quality
gingivaUBERON:000182890.18gold quality
oral cavityUBERON:000016790.12gold quality
duodenumUBERON:000211489.95gold quality
mucosa of sigmoid colonUBERON:000499389.95gold quality
colonic mucosaUBERON:000031789.79gold quality
gingival epitheliumUBERON:000194989.78gold quality
vastus lateralisUBERON:000137989.09gold quality
spermCL:000001989.03gold quality
quadriceps femorisUBERON:000137788.98silver quality
bone marrowUBERON:000237188.80gold quality
tendonUBERON:000004388.74gold quality
liverUBERON:000210788.68gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-4yes35.69
E-HCAD-5yes32.58
E-ANND-3yes13.92
E-MTAB-9388yes10.39
E-GEOD-135922yes7.07
E-MTAB-8060no237.84
E-MTAB-6524no196.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting SYAP1, 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-9-5P100.0072.282361
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3924100.0072.092394
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-186-5P99.9970.833707
HSA-MIR-428299.9975.366408
HSA-MIR-223-3P99.9970.141140
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-590-3P99.9674.346478
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-144-3P99.9473.982698
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-205-3P99.9269.923165
HSA-MIR-61399.9171.501710
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-380-3P99.8970.181978
HSA-MIR-153-5P99.8973.866317
HSA-MIR-4671-3P99.8872.461045
HSA-MIR-221-5P99.8665.451052

Literature-anchored findings (GeneRIF, showing 1)

  • BSTA (SYAP!) promotes mTORC2-mediated phosphorylation of Akt1 to suppress expression of FoxC2 and stimulate adipocyte differentiation. (PMID:23300339)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosyap1ENSDARG00000012946
mus_musculusSyap1ENSMUSG00000031357
rattus_norvegicusSyap1ENSRNOG00000004304
drosophila_melanogasterSap47FBGN0013334
caenorhabditis_elegansC16C2.4WBGENE00007621

Paralogs (1): BSDC1 (ENSG00000160058)

Protein

Protein identifiers

Synapse-associated protein 1Q96A49 (reviewed: Q96A49)

Alternative names: BSD domain-containing signal transducer and Akt interactor protein

All UniProt accessions (1): Q96A49

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in adipocyte differentiation by promoting mTORC2-mediated phosphorylation of AKT1 at ‘Ser-473’ after growth factor stimulation.

Subunit / interactions. Interacts (via phosphorylated form and BSD domain) with AKT1; this interaction is enhanced in a mTORC2-mediated manner in response to epidermal growth factor (EGF) stimulation and activates AKT1.

Subcellular location. Cytoplasm. Perinuclear region. Golgi apparatus. Perikaryon. Cell projection. Axon. Dendrite. Growth cone. Presynaptic cell membrane. Postsynaptic cell membrane. Membrane.

Tissue specificity. Expressed in heart, placenta, lung, liver, skeletal muscle, kidney and pancreas.

Post-translational modifications. Phosphorylated. Phosphorylation increases in a mTORC2-mediated manner in response to epidermal growth factor (EGF) stimulation.

RefSeq proteins (1): NP_116185* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005607BSD_domDomain
IPR035925BSD_dom_sfHomologous_superfamily
IPR051494BSD_domain-containingFamily

Pfam: PF03909

UniProt features (17 total): helix 5, modified residue 3, sequence conflict 3, chain 1, domain 1, strand 1, turn 1, region of interest 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1X3ASOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96A49-F166.180.24

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 (3): 248, 269, 313

Mutagenesis-validated functional residues (1):

PositionPhenotype
198–199inhibits interaction with akt1, mtorc2-mediated phosphorylation of akt1 at ‘ser-473’ and adipocyte differentiation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_FAT_CELL_DIFFERENTIATION, TAATAAT_MIR126, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_REGULATION_OF_NEURONAL_SYNAPTIC_PLASTICITY, GOBP_POSITIVE_REGULATION_OF_FAT_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_SHORT_TERM_NEURONAL_SYNAPTIC_PLASTICITY, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_RESPONSE_TO_EPIDERMAL_GROWTH_FACTOR, GOBP_CELLULAR_RESPONSE_TO_INSULIN_STIMULUS, GOBP_CELL_CELL_SIGNALING, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY

GO Biological Process (9): cell differentiation (GO:0030154), cellular response to insulin stimulus (GO:0032869), cellular response to platelet-derived growth factor stimulus (GO:0036120), TORC2 signaling (GO:0038203), positive regulation of fat cell differentiation (GO:0045600), regulation of short-term neuronal synaptic plasticity (GO:0048172), cellular response to epidermal growth factor stimulus (GO:0071364), positive regulation of protein serine/threonine kinase activity (GO:0071902), cellular response to insulin-like growth factor stimulus (GO:1990314)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (18): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), cytosol (GO:0005829), cytoplasmic side of plasma membrane (GO:0009898), axon (GO:0030424), dendrite (GO:0030425), growth cone (GO:0030426), presynaptic membrane (GO:0042734), perikaryon (GO:0043204), synapse (GO:0045202), postsynaptic membrane (GO:0045211), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure7
cytoplasm3
cellular response to peptide hormone stimulus2
cellular response to growth factor stimulus2
intracellular membrane-bounded organelle2
neuron projection2
synaptic membrane2
cellular developmental process1
response to insulin1
response to platelet-derived growth factor1
TOR signaling1
fat cell differentiation1
positive regulation of cell differentiation1
regulation of fat cell differentiation1
regulation of neuronal synaptic plasticity1
response to epidermal growth factor1
protein serine/threonine kinase activity1
positive regulation of protein kinase activity1
regulation of protein serine/threonine kinase activity1
binding1
nuclear lumen1
intracellular anatomical structure1
endomembrane system1
plasma membrane1
cytoplasmic side of membrane1
dendritic tree1
site of polarized growth1
distal axon1
presynapse1
neuronal cell body1
cell junction1
postsynapse1
extracellular vesicle1
membrane1
cell periphery1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYAP1NOC4LQ9BVI4480
SYAP1CTPS2Q9NRF8461
SYAP1TXLNGQ9NUQ3456
SYAP1REPS2Q8NFH8438
SYAP1EIF2S3P41091429
SYAP1RICTORQ6R327419
SYAP1CA5BQ9Y2D0403
SYAP1AP1S2P56377372
SYAP1CCDC125Q86Z20363
SYAP1ATP5MEP56385360
SYAP1ZRSR2Q15696357
SYAP1FAM9AQ8IZU1357
SYAP1PUDPQ08623355
SYAP1DTX3Q8N9I9355
SYAP1PABIR2Q7Z309352

IntAct

95 interactions, top by confidence:

ABTypeScore
MFN1MFN2psi-mi:“MI:0914”(association)0.790
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
SYAP1PIN1psi-mi:“MI:0915”(physical association)0.690
PIN1POLR2Dpsi-mi:“MI:0914”(association)0.640
SYAP1NDNpsi-mi:“MI:0915”(physical association)0.600
IGF1RPIK3R2psi-mi:“MI:2364”(proximity)0.590
INSRPIK3R2psi-mi:“MI:2364”(proximity)0.570
SLC39A1NME2P1psi-mi:“MI:0914”(association)0.560
THRASYAP1psi-mi:“MI:0915”(physical association)0.560
TNFRSF10CSYAP1psi-mi:“MI:0915”(physical association)0.560
MIPSYAP1psi-mi:“MI:0915”(physical association)0.560
ZFPL1SYAP1psi-mi:“MI:0915”(physical association)0.560
ADIPOQSYAP1psi-mi:“MI:0915”(physical association)0.560
SNRNP27UBA6psi-mi:“MI:0914”(association)0.530
TAS2R41YKT6psi-mi:“MI:0914”(association)0.530
USP47DENRpsi-mi:“MI:0914”(association)0.530
CYP1A1SNX3psi-mi:“MI:0914”(association)0.530
BAG2HGSpsi-mi:“MI:0914”(association)0.530
POT1SYAP1psi-mi:“MI:0915”(physical association)0.510
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
OTUB1EPM2Apsi-mi:“MI:0914”(association)0.350
EcdAAR2psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350

BioGRID (194): SYAP1 (Co-fractionation), SYAP1 (Co-fractionation), SYAP1 (Co-fractionation), SYAP1 (Proximity Label-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-RNA), SYAP1 (Proximity Label-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS), PIN1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS), SYAP1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNJ3, A0M8T5, A0PJT0, A2BIJ3, D3ZTQ1, O35867, O94876, P42566, P42567, P97578, Q00PJ1, Q02225, Q09YI1, Q09YK4, Q09YM8, Q16643, Q2IBF8, Q2QL82, Q2QLA2, Q2QLG9, Q2T9N1, Q3SX22, Q3UQU0, Q3USH5, Q5BJ78, Q5RDH2, Q5T1M5, Q5U3K5, Q5ZIK6, Q68EF0, Q69ZZ6, Q6INU2, Q6NTW1, Q6P9Q6, Q6TYB5, Q6ZPJ0, Q80Y55, Q8IWB9, Q8IWE2, Q8N0X7

Diamond homologs: Q960T2, Q96A49, Q9D5V6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 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 Cancer58.1×4e-03
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling67.4×2e-03
RAF/MAP kinase cascade86.3×9e-04
PIP3 activates AKT signaling76.0×2e-03

GO biological processes:

GO termPartnersFoldFDR
obsolete protein targeting to mitochondrion532.3×4e-04
MAPK cascade610.2×5e-03
protein autophosphorylation69.7×5e-03
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction97.8×1e-03
positive regulation of MAPK cascade87.2×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1062 predictions. Top by Δscore:

VariantEffectΔscore
X:16719895:CGGCA:Cdonor_gain1.0000
X:16719896:GGCA:Gdonor_gain1.0000
X:16719896:GGCAG:Gdonor_gain1.0000
X:16719897:GCA:Gdonor_gain1.0000
X:16719897:GCAG:Gdonor_gain1.0000
X:16719900:G:GGdonor_gain1.0000
X:16735216:A:AGacceptor_gain1.0000
X:16735223:ACAG:Aacceptor_loss1.0000
X:16735224:C:Gacceptor_gain1.0000
X:16735224:CA:Cacceptor_loss1.0000
X:16735225:A:AGacceptor_gain1.0000
X:16735226:G:GTacceptor_gain1.0000
X:16735226:GA:Gacceptor_gain1.0000
X:16735226:GAC:Gacceptor_gain1.0000
X:16735226:GACT:Gacceptor_gain1.0000
X:16735226:GACTA:Gacceptor_gain1.0000
X:16735342:CAAG:Cdonor_loss1.0000
X:16735343:AAG:Adonor_loss1.0000
X:16735344:AG:Adonor_loss1.0000
X:16735346:G:Tdonor_loss1.0000
X:16736163:CA:Cacceptor_loss1.0000
X:16736164:A:AGacceptor_gain1.0000
X:16736164:A:ATacceptor_loss1.0000
X:16736165:G:GGacceptor_gain1.0000
X:16736165:G:GTacceptor_loss1.0000
X:16736165:GA:Gacceptor_gain1.0000
X:16736165:GAC:Gacceptor_gain1.0000
X:16736165:GACA:Gacceptor_gain1.0000
X:16736228:GTCAG:Gdonor_gain1.0000
X:16741696:T:TAacceptor_gain1.0000

AlphaMissense

2340 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:16741733:T:AW127R1.000
X:16741733:T:CW127R1.000
X:16754964:T:AW199R1.000
X:16754964:T:CW199R1.000
X:16754992:T:CL208P1.000
X:16741735:G:CW127C0.999
X:16741735:G:TW127C0.999
X:16743714:T:CF150S0.999
X:16743777:C:AA171D0.999
X:16743821:T:CF186L0.999
X:16743823:T:AF186L0.999
X:16743823:T:GF186L0.999
X:16743831:T:AV189D0.999
X:16754962:T:CF198S0.999
X:16754979:T:GY204D0.999
X:16754982:C:AR205S0.999
X:16754983:G:CR205P0.999
X:16754988:T:CS207P0.999
X:16735254:C:AA68D0.998
X:16741782:T:CL143S0.998
X:16743720:G:CR152P0.998
X:16743797:G:CD178H0.998
X:16743807:T:CL181P0.998
X:16743819:G:CR185T0.998
X:16743820:A:CR185S0.998
X:16743820:A:TR185S0.998
X:16743828:T:CL188P0.998
X:16754961:T:CF198L0.998
X:16754963:C:AF198L0.998
X:16754963:C:GF198L0.998

dbSNP variants (sampled 300 via entrez): RS1000062367 (X:16718514 T>TC), RS1000273744 (X:16756330 T>A,G), RS1000291529 (X:16750245 T>C,G), RS1000324605 (X:16750491 G>C), RS1000413728 (X:16719243 G>A,C), RS1000466344 (X:16725452 G>C), RS1000488490 (X:16743233 C>T), RS1000536607 (X:16757831 C>T), RS1000636814 (X:16748137 G>A,T), RS1000773417 (X:16740011 G>A,C), RS1000839465 (X:16742058 C>G,T), RS1000839559 (X:16744075 A>G), RS1000961390 (X:16758179 G>C), RS1001020511 (X:16721498 C>T), RS1001300507 (X:16752491 C>G)

Disease associations

OMIM: gene `` | 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

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression3
Valproic Acidincreases expression2
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
arseniteaffects binding, increases reaction1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Smokedecreases expression1
Testosteronedecreases expression1
Thiramincreases expression1
Aflatoxin B1increases expression1
Cadmium Chlorideincreases expression1
Okadaic Acidincreases expression1
Lactic Aciddecreases expression1
Genisteindecreases expression, increases reaction1
Particulate Matterincreases abundance, increases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3ISAbcam HEK293T SYAP1 KOTransformed cell lineFemale

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.