SERINC3

gene
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Also known as DIFF33TDESBBI99TMS-1AIGP1

Summary

SERINC3 (serine incorporator 3, HGNC:11699) is a protein-coding gene on chromosome 20q13.12, encoding Serine incorporator 3 (Q13530). Restriction factor required to restrict infectivity of lentiviruses, such as HIV-1: acts by inhibiting an early step of viral infection.

Enables phospholipid scramblase activity. Involved in antiviral innate immune response and plasma membrane phospholipid scrambling. Located in plasma membrane.

Source: NCBI Gene 10955 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 90 total
  • MANE Select transcript: NM_006811

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11699
Approved symbolSERINC3
Nameserine incorporator 3
Location20q13.12
Locus typegene with protein product
StatusApproved
AliasesDIFF33, TDE, SBBI99, TMS-1, AIGP1
Ensembl geneENSG00000132824
Ensembl biotypeprotein_coding
OMIM607165
Entrez10955

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 16 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000255175, ENST00000342374, ENST00000411544, ENST00000468234, ENST00000885443, ENST00000885444, ENST00000885445, ENST00000885446, ENST00000885447, ENST00000885448, ENST00000885449, ENST00000885450, ENST00000930100, ENST00000930101, ENST00000967986, ENST00000967987, ENST00000967988

RefSeq mRNA: 2 — MANE Select: NM_006811 NM_006811, NM_198941

CCDS: CCDS13333

Canonical transcript exons

ENST00000342374 — 10 exons

ExonStartEnd
ENSE000009068794450107344501300
ENSE000009068804450381544503995
ENSE000009068814450480144504891
ENSE000009068824450682744506996
ENSE000009068834450989144510028
ENSE000009068844451128944511368
ENSE000009068854451280144512994
ENSE000013908124449744144500434
ENSE000018783414452191344522070
ENSE000036142664451387944514040

Expression profiles

Bgee: expression breadth ubiquitous, 304 present calls, max score 98.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 100.1554 / max 1086.0779, expressed in 1822 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18734799.98151822
1873450.096836
1873460.077031

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011598.84gold quality
tendon of biceps brachiiUBERON:000818898.81gold quality
ponsUBERON:000098898.47gold quality
medial globus pallidusUBERON:000247798.24gold quality
Brodmann (1909) area 23UBERON:001355498.23gold quality
middle temporal gyrusUBERON:000277198.17gold quality
tendonUBERON:000004398.09gold quality
superior frontal gyrusUBERON:000266198.04gold quality
stromal cell of endometriumCL:000225598.02gold quality
globus pallidusUBERON:000187597.94gold quality
postcentral gyrusUBERON:000258197.83gold quality
prefrontal cortexUBERON:000045197.82gold quality
orbitofrontal cortexUBERON:000416797.81gold quality
Brodmann (1909) area 46UBERON:000648397.81gold quality
parietal lobeUBERON:000187297.80gold quality
superior vestibular nucleusUBERON:000722797.79gold quality
trigeminal ganglionUBERON:000167597.75gold quality
calcaneal tendonUBERON:000370197.69gold quality
right testisUBERON:000453497.64gold quality
left testisUBERON:000453397.62gold quality
adult organismUBERON:000702397.59gold quality
islet of LangerhansUBERON:000000697.55gold quality
inferior vagus X ganglionUBERON:000536397.50gold quality
dorsal root ganglionUBERON:000004497.49gold quality
placentaUBERON:000198797.42gold quality
entorhinal cortexUBERON:000272897.42gold quality
vena cavaUBERON:000408797.42gold quality
cauda epididymisUBERON:000436097.36gold quality
subthalamic nucleusUBERON:000190697.33gold quality
occipital lobeUBERON:000202197.32gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-13yes11.73
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GABPA

miRNA regulators (miRDB)

135 targeting SERINC3, 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-1277-5P100.0073.955056
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-656-3P100.0072.152788
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-186-5P99.9970.833707
HSA-MIR-371B-5P99.9975.344759
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-9-3P99.9670.882068
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548J-3P99.9472.614881

Literature-anchored findings (GeneRIF, showing 4)

  • TDE1 inhibits apoptosis and stimulates tumorigenesis (PMID:16547497)
  • SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef (PMID:26416733)
  • In MOLT-3 cells, Nef remained crucial for HIV-1 replication even in the absence of SERINC3 and SERINC5. (PMID:31186327)
  • HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo-electron and TIRF microscopy. (PMID:32788212)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioSERINC3ENSDARG00000086133
danio_reriosi:ch73-267c23.10ENSDARG00000111669
mus_musculusSerinc3ENSMUSG00000017707
rattus_norvegicusSerinc3ENSRNOG00000009552
drosophila_melanogasterSerincFBGN0028399
caenorhabditis_elegansWBGENE00011250
caenorhabditis_elegansWBGENE00021956

Paralogs (4): SERINC1 (ENSG00000111897), SERINC5 (ENSG00000164300), SERINC2 (ENSG00000168528), SERINC4 (ENSG00000184716)

Protein

Protein identifiers

Serine incorporator 3Q13530 (reviewed: Q13530)

Alternative names: Tumor differentially expressed protein 1

All UniProt accessions (2): Q13530, Q5H936

UniProt curated annotations — full annotation on UniProt →

Function. Restriction factor required to restrict infectivity of lentiviruses, such as HIV-1: acts by inhibiting an early step of viral infection. Impairs the penetration of the viral particle into the cytoplasm. Non-ATP-dependent, non-specific lipid transporter for phosphatidylserine, phosphatidylcholine, and phosphatidylethanolamine. Functions as a scramblase that flips lipids in both directions across the membrane. Phospholipid scrambling results in HIV-1 surface exposure of phosphatidylserine and loss of membrane asymmetry, which leads to changes in HIV-1 Env conformation and loss of infectivity.

Subcellular location. Cell membrane. Golgi apparatus membrane Cytoplasm. Perinuclear region.

Tissue specificity. Ubiquitous. Expression levels were increased fourfold to tenfold in lung tumor tissues compared with normal pulmonary tissues.

Post-translational modifications. N-glycosylated.

Similarity. Belongs to the TDE1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13530-11yes
Q13530-22

RefSeq proteins (2): NP_006802, NP_945179 (=MANE)

Domains & families (InterPro)

IDNameType
IPR005016TDE1/TMSFamily

Pfam: PF03348

Catalyzed reactions (Rhea), 3 shown:

  • a 1,2-diacyl-sn-glycero-3-phosphocholine(in) = a 1,2-diacyl-sn-glycero-3-phosphocholine(out) (RHEA:38571)
  • a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out) (RHEA:38663)
  • a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(in) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(out) (RHEA:38895)

UniProt features (22 total): topological domain 9, transmembrane region 8, chain 1, modified residue 1, glycosylation site 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
7RU6ELECTRON MICROSCOPY4.4
7RUGELECTRON MICROSCOPY4.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13530-F177.550.45

Antibody-complex structures (SAbDab): 27RU6, 7RUG

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): 371

Glycosylation sites (1): 34

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-977347Serine metabolism
R-HSA-1430728Metabolism
R-HSA-71291Metabolism of amino acids and derivatives

MSigDB gene sets: 305 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, FREAC2_01, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOLDRATH_ANTIGEN_RESPONSE, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, MARTINEZ_RB1_TARGETS_UP, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_REGULATION_OF_ENDOPLASMIC_RETICULUM_STRESS_INDUCED_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY

GO Biological Process (9): L-serine metabolic process (GO:0006563), plasma membrane phospholipid scrambling (GO:0017121), antiviral innate immune response (GO:0140374), positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237), immune system process (GO:0002376), L-serine biosynthetic process (GO:0006564), L-serine transport (GO:0015825), innate immune response (GO:0045087), defense response to virus (GO:0051607)

GO Molecular Function (4): phospholipid scramblase activity (GO:0017128), molecular carrier activity (GO:0140104), protein binding (GO:0005515), L-serine transmembrane transporter activity (GO:0015194)

GO Cellular Component (6): Golgi membrane (GO:0000139), plasma membrane (GO:0005886), membrane (GO:0016020), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Metabolism of amino acids and derivatives1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
binding2
cytoplasm2
L-amino acid metabolic process1
proteinogenic amino acid metabolic process1
plasma membrane organization1
phospholipid translocation1
innate immune response1
defense response to virus1
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress1
regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway1
positive regulation of response to endoplasmic reticulum stress1
positive regulation of intrinsic apoptotic signaling pathway1
biological_process1
L-serine metabolic process1
serine family amino acid biosynthetic process1
L-amino acid biosynthetic process1
proteinogenic amino acid biosynthetic process1
L-amino acid transport1
serine transport1
immune response1
defense response to symbiont1
defense response1
response to virus1
plasma membrane phospholipid scrambling1
intramembrane lipid carrier activity1
molecular_function1
L-amino acid transmembrane transporter activity1
L-serine transport1
Golgi apparatus1
bounding membrane of organelle1
membrane1
cell periphery1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

794 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SERINC3GRXCR1A8MXD5892
SERINC3BST2Q10589591
SERINC3SAMHD1Q9Y3Z3578
SERINC3RUSC2Q8N2Y8572
SERINC3TRIM5Q9C035554
SERINC3GLRXP35754548
SERINC3MARCHF2Q9P0N8524
SERINC3RUSC1Q9BVN2516
SERINC3APOBEC3GQ9HC16511
SERINC3AP4E1Q9UPM8509
SERINC3MX2P20592508
SERINC3CCR5P51681503
SERINC3CXCR4P30991474
SERINC3ATG9AQ7Z3C6471
SERINC3D6RGC4D6RGC4470

IntAct

30 interactions, top by confidence:

ABTypeScore
GRNSERINC3psi-mi:“MI:0915”(physical association)0.560
SERINC3PEX1psi-mi:“MI:0915”(physical association)0.560
SERINC3WFS1psi-mi:“MI:0915”(physical association)0.560
SERINC3TRIM28psi-mi:“MI:0915”(physical association)0.400
SERINC3AGTR1psi-mi:“MI:0915”(physical association)0.370
SERINC3DRD2psi-mi:“MI:0915”(physical association)0.370
SERINC3RPS15psi-mi:“MI:0915”(physical association)0.370
SERINC3BMP10psi-mi:“MI:0915”(physical association)0.370
Trappc8TRAPPC13psi-mi:“MI:0914”(association)0.350
P2RY1EI24psi-mi:“MI:0914”(association)0.350
CAPRIN1VPS37Cpsi-mi:“MI:0914”(association)0.350
CAPRIN1SDCBPpsi-mi:“MI:0914”(association)0.350
EIF4A1SNAP23psi-mi:“MI:0914”(association)0.350
SURF4SERINC3psi-mi:“MI:0915”(physical association)0.000
SERINC3KDELR1psi-mi:“MI:0915”(physical association)0.000
SERINC3PHB2psi-mi:“MI:0915”(physical association)0.000
SERINC3HACD3psi-mi:“MI:0915”(physical association)0.000
SERINC3SLC16A1psi-mi:“MI:0915”(physical association)0.000
SERINC3VDAC3psi-mi:“MI:0915”(physical association)0.000
SERINC3KDELR2psi-mi:“MI:0915”(physical association)0.000
SERINC3XPO5psi-mi:“MI:0915”(physical association)0.000
SERINC3VDAC2psi-mi:“MI:0915”(physical association)0.000

BioGRID (23): SERINC3 (Affinity Capture-MS), XPO5 (Affinity Capture-MS), PHB2 (Affinity Capture-MS), SURF4 (Affinity Capture-MS), VDAC2 (Affinity Capture-MS), KDELR1 (Affinity Capture-MS), PTPLAD1 (Affinity Capture-MS), SLC16A1 (Affinity Capture-MS), KDELR2 (Affinity Capture-MS), SERINC3 (Proximity Label-MS), SERINC3 (Affinity Capture-MS), SERINC3 (Two-hybrid), SERINC3 (Two-hybrid), SERINC3 (Affinity Capture-MS), SERINC3 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDC7, A4FUZ5, A9CAZ8, B9TRX0, O15243, O89013, O95807, P04116, P23289, P23294, P36963, P36965, P47789, P47790, P56557, P60201, P60202, P60203, Q0P442, Q0P467, Q13491, Q13530, Q1E1E0, Q3SYT0, Q3SZL9, Q3T110, Q3ZC23, Q4R6L9, Q561T9, Q566G2, Q5PSV5, Q5R4C3, Q5R533, Q5R603, Q5R6E6, Q5ZJD9, Q712P7, Q7TNK0, Q7Z0Q2, Q803X0

Diamond homologs: A4FUZ5, A6NH21, A7S4N4, A8WCG0, A9UY97, Q12116, Q13530, Q3MHV9, Q4R6L9, Q54UF8, Q58CW5, Q5R419, Q5R533, Q5XK03, Q63175, Q7TNK0, Q803X0, Q86VE9, Q8BHJ6, Q8K0E7, Q96SA4, Q9HDY3, Q9NRX5, Q9QZI8, Q9QZI9

SIGNOR signaling

2 interactions.

AEffectBMechanism
CSNK2A1“up-regulates activity”SERINC3phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance62
Likely benign9
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1637 predictions. Top by Δscore:

VariantEffectΔscore
20:44500430:CAGGG:Cacceptor_gain1.0000
20:44500435:C:CCacceptor_gain1.0000
20:44501149:A:ACdonor_gain1.0000
20:44501150:C:CCdonor_gain1.0000
20:44501157:C:CAdonor_gain1.0000
20:44501315:C:CTacceptor_gain1.0000
20:44501315:C:Tacceptor_gain1.0000
20:44501316:A:Tacceptor_gain1.0000
20:44503863:T:Cdonor_gain1.0000
20:44503883:A:ACdonor_gain1.0000
20:44503884:C:CCdonor_gain1.0000
20:44503884:CT:Cdonor_gain1.0000
20:44503992:CGAT:Cacceptor_gain1.0000
20:44503994:ATCTG:Aacceptor_loss1.0000
20:44503995:TC:Tacceptor_loss1.0000
20:44503996:C:CCacceptor_gain1.0000
20:44503996:CTGAA:Cacceptor_loss1.0000
20:44503997:T:Gacceptor_loss1.0000
20:44509887:CTA:Cdonor_loss1.0000
20:44509888:TA:Tdonor_loss1.0000
20:44509890:C:CAdonor_loss1.0000
20:44509890:CCAG:Cdonor_gain1.0000
20:44510024:CCAGA:Cacceptor_gain1.0000
20:44510025:CAGA:Cacceptor_gain1.0000
20:44510025:CAGAC:Cacceptor_gain1.0000
20:44510026:AGA:Aacceptor_gain1.0000
20:44510027:GA:Gacceptor_gain1.0000
20:44510029:C:CCacceptor_gain1.0000
20:44512797:ATAC:Adonor_loss1.0000
20:44512798:TA:Tdonor_loss1.0000

AlphaMissense

3112 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:44500368:G:CS450R0.996
20:44500368:G:TS450R0.996
20:44500370:T:GS450R0.996
20:44511353:T:AK137N0.996
20:44511353:T:GK137N0.996
20:44511364:A:GW134R0.996
20:44511364:A:TW134R0.996
20:44500367:A:GW451R0.995
20:44500367:A:TW451R0.995
20:44500343:A:GW459R0.994
20:44500343:A:TW459R0.994
20:44500302:G:CF472L0.992
20:44500302:G:TF472L0.992
20:44500304:A:GF472L0.992
20:44506846:G:CS255W0.992
20:44506868:A:GC248R0.992
20:44506884:A:CS242R0.992
20:44506884:A:TS242R0.992
20:44506886:T:GS242R0.992
20:44500330:G:TA463D0.991
20:44509991:G:CF171L0.991
20:44509991:G:TF171L0.991
20:44509993:A:GF171L0.991
20:44511354:T:AK137I0.991
20:44509956:G:TA183D0.990
20:44504818:G:TA286D0.989
20:44506878:G:CN244K0.989
20:44506878:G:TN244K0.989
20:44509977:A:GL176P0.989
20:44511355:T:CK137E0.989

dbSNP variants (sampled 300 via entrez): RS1000174768 (20:44513250 C>A), RS1000245326 (20:44523000 G>A), RS1000255314 (20:44508252 G>A,C), RS1000283629 (20:44517069 T>C), RS1000289603 (20:44504530 C>T), RS1000352638 (20:44501398 C>T), RS1000566066 (20:44512131 G>A), RS1000765317 (20:44503193 A>T), RS1000831035 (20:44501717 C>T), RS1000931522 (20:44496662 C>G,T), RS1001029847 (20:44505704 T>C), RS1001093133 (20:44502882 C>T), RS1001160868 (20:44499716 T>G), RS1001168940 (20:44521159 G>C,T), RS1001249045 (20:44517145 C>G)

Disease associations

OMIM: gene MIM:607165 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST000964_28Ulcerative colitis1.000000e-20
GCST001647_15Bipolar disorder9.000000e-06
GCST004131_41Inflammatory bowel disease1.000000e-17
GCST004133_4Ulcerative colitis4.000000e-30

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, affects expression, decreases expression3
Ozoneaffects cotreatment, increases oxidation, increases abundance, affects expression2
FR900359decreases phosphorylation1
bisphenol Faffects cotreatment, increases expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
glycidyl methacrylateincreases expression1
sodium arseniteincreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
K 7174increases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Asbestosaffects expression1
Caffeineincreases phosphorylation1
Dexamethasoneincreases expression, affects cotreatment1
Doxorubicindecreases expression1
Formaldehydeincreases expression1
Indomethacinaffects cotreatment, increases expression1
Leadaffects expression1
Nicotineincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Vitamin Eincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Sodium Seleniteincreases expression1
Particulate Matterincreases abundance, decreases expression1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

Clinical trials (associated diseases)

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