SYNE3

gene
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Also known as FLJ25605NET53Nesprin-3Nesp3

Summary

SYNE3 (spectrin repeat containing nuclear envelope family member 3, HGNC:19861) is a protein-coding gene on chromosome 14q32.13, encoding Nesprin-3 (Q6ZMZ3). As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton.

Enables actin filament binding activity and cytoskeleton-nuclear membrane anchor activity. Involved in cytoskeleton organization; establishment of protein localization to membrane; and regulation of cell shape. Located in nuclear membrane. Part of meiotic nuclear membrane microtubule tethering complex. Biomarker of Huntington’s disease.

Source: NCBI Gene 161176 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 195 total
  • MANE Select transcript: NM_152592

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19861
Approved symbolSYNE3
Namespectrin repeat containing nuclear envelope family member 3
Location14q32.13
Locus typegene with protein product
StatusApproved
AliasesFLJ25605, NET53, Nesprin-3, Nesp3
Ensembl geneENSG00000176438
Ensembl biotypeprotein_coding
OMIM610861
Entrez161176

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 15 protein_coding, 1 retained_intron

ENST00000334258, ENST00000553340, ENST00000554873, ENST00000555759, ENST00000557275, ENST00000682763, ENST00000908202, ENST00000908203, ENST00000965383, ENST00000965384, ENST00000965385, ENST00000965386, ENST00000965387, ENST00000965388, ENST00000965389, ENST00000965390

RefSeq mRNA: 6 — MANE Select: NM_152592 NM_001363692, NM_001384281, NM_001384282, NM_001384283, NM_001384284, NM_152592

CCDS: CCDS86430, CCDS91927, CCDS9935

Canonical transcript exons

ENST00000682763 — 18 exons

ExonStartEnd
ENSE000010937409545224795452383
ENSE000012281659543207995432117
ENSE000012281719543326095433409
ENSE000012281769543682095436981
ENSE000012282109544993195450105
ENSE000013272789543903395439162
ENSE000013338279546779595467967
ENSE000019315179540726695418026
ENSE000034613979544448595444628
ENSE000034956749543961295439784
ENSE000035647539545537795455724
ENSE000036191649546593195466240
ENSE000036264379543991495440075
ENSE000036403609544590995446091
ENSE000036630249544315595443289
ENSE000036847389545717795457338
ENSE000039180509551659695516650
ENSE000039190239547567895475835

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 98.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1792 / max 90.5442, expressed in 1322 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1447915.79081290
1447920.201393
1447890.099349
1447880.087850

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818898.61gold quality
parietal pleuraUBERON:000240097.73gold quality
layer of synovial tissueUBERON:000761697.30gold quality
trabecular bone tissueUBERON:000248396.82gold quality
pleuraUBERON:000097796.55gold quality
synovial jointUBERON:000221796.34gold quality
skin of hipUBERON:000155495.34gold quality
visceral pleuraUBERON:000240194.76gold quality
superficial temporal arteryUBERON:000161493.70gold quality
tendonUBERON:000004392.77gold quality
pericardiumUBERON:000240792.53gold quality
upper leg skinUBERON:000426292.21gold quality
sural nerveUBERON:001548891.80gold quality
mammary ductUBERON:000176591.39gold quality
tibiaUBERON:000097990.48gold quality
periodontal ligamentUBERON:000826690.17gold quality
thoracic mammary glandUBERON:000520090.04gold quality
mammary glandUBERON:000191189.99gold quality
calcaneal tendonUBERON:000370189.96gold quality
epithelium of mammary glandUBERON:000324489.41gold quality
medial globus pallidusUBERON:000247789.11gold quality
lower lobe of lungUBERON:000894988.94gold quality
upper arm skinUBERON:000426388.47gold quality
connective tissueUBERON:000238488.19gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451188.13gold quality
mammalian vulvaUBERON:000099788.08gold quality
subcutaneous adipose tissueUBERON:000219088.05gold quality
adipose tissueUBERON:000101387.99gold quality
dorsal motor nucleus of vagus nerveUBERON:000287087.39gold quality
globus pallidusUBERON:000187587.33gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9067yes11.89
E-ANND-3yes7.39
E-MTAB-7303no210.28
E-MTAB-5061no3.45

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP63

miRNA regulators (miRDB)

34 targeting SYNE3, 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-3163100.0077.238605
HSA-MIR-453499.9966.581907
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1213699.9872.815713
HSA-MIR-56899.9869.862084
HSA-MIR-548N99.9871.944170
HSA-MIR-808299.9567.271170
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-76599.8468.242442
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-46699.6770.852863
HSA-MIR-464399.4967.631791
HSA-MIR-519D-5P99.4169.302057
HSA-MIR-568399.3668.592083
HSA-MIR-319999.1765.19696
HSA-MIR-805299.1765.01719
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-1288-5P98.8567.01734
HSA-MIR-393898.7266.07834
HSA-MIR-3145-5P98.5767.83900
HSA-MIR-6827-5P98.4664.881256
HSA-MIR-444398.0266.251928
HSA-MIR-6883-3P97.9767.35643
HSA-MIR-430597.9468.63533

Literature-anchored findings (GeneRIF, showing 9)

  • association with human nesprin-3 appeared to be stronger for torsinADeltaE than for torsinA. TorsinA also associated with the KASH domains of nesprin-1 and -2 (PMID:18827015)
  • nesprin-3 regulates vascular endothelial cell shape, perinuclear cytoskeletal architecture, and important aspects of flow-mediated mechanotransduction. (PMID:21937718)
  • Meta-analysis estimated the relationship between LINC00341 expression and distant metastasis or lymph node metastasis in breast cancer. (PMID:28146429)
  • Overexpression of LINC00341 suppresses the expression of vascular cell adhesion molecule 1 (VCAM1) and the adhesion of monocytes induced by atheroprone flow and tumor necrosis factor-alpha. (PMID:28500253)
  • SPAG4, in cooperation with Nesprin3, has a fundamental pathological function in the migration of lung carcinoma cells. (PMID:29901114)
  • LINC00341 interacts with miR-141 to suppress its functional binding to the 3’-untranslated region of YAF2 messenger RNA whereby supporting chondrocyte survival and preventing osteoarthritis progression. (PMID:30672021)
  • Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis. (PMID:32700968)
  • Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors. (PMID:32948197)
  • Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes. (PMID:33058875)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosyne3ENSDARG00000023237
mus_musculusSyne3ENSMUSG00000054150
rattus_norvegicusSyne3ENSRNOG00000005287

Paralogs (36): SYNE2 (ENSG00000054654), SPTB (ENSG00000070182), ACTN1 (ENSG00000072110), ACTN2 (ENSG00000077522), DSP (ENSG00000096696), DRP2 (ENSG00000102385), SPTBN1 (ENSG00000115306), MACF1 (ENSG00000127603), FLNC (ENSG00000128591), ACTN4 (ENSG00000130402), SYNE1 (ENSG00000131018), MICAL2 (ENSG00000133816), DTNA (ENSG00000134769), MICAL1 (ENSG00000135596), FLNB (ENSG00000136068), SPTBN5 (ENSG00000137877), DTNB (ENSG00000138101), GAS2L3 (ENSG00000139354), DST (ENSG00000151914), UTRN (ENSG00000152818), SPTBN4 (ENSG00000160460), SPTA1 (ENSG00000163554), CLMN (ENSG00000165959), PKHD1 (ENSG00000170927), SPTBN2 (ENSG00000173898), PLEC (ENSG00000178209), SMTNL2 (ENSG00000188176), FLNA (ENSG00000196924), SPTAN1 (ENSG00000197694), DMD (ENSG00000198947), PKHD1L1 (ENSG00000205038), DYTN (ENSG00000232125), MICAL3 (ENSG00000243156), ACTN3 (ENSG00000248746), EPPK1 (ENSG00000261150), GAS2L2 (ENSG00000270765)

Protein

Protein identifiers

Nesprin-3Q6ZMZ3 (reviewed: Q6ZMZ3)

Alternative names: KASH domain-containing protein 3, Nuclear envelope spectrin repeat protein 3

All UniProt accessions (2): Q6ZMZ3, G3V533

UniProt curated annotations — full annotation on UniProt →

Function. As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells.

Subunit / interactions. Core component of LINC complexes which are composed of inner nuclear membrane SUN domain-containing proteins coupled to outer nuclear membrane KASH domain-containing nesprins. SUN and KASH domain-containing proteins seem to bind each other promiscuously; however, differentially expression of LINC complex constituents can give rise to specific assemblies. Interacts with SUN1 and SUN2; probably forming respective LINC complexes. Interacts with PLEC (via actin-binding domain). Interacts with DST. Interacts with SYNE1 via spectrin repeats. Interacts (via KASH domain) with TOR1A (ATP-bound); the interaction is required for SYNE3 nuclear envelope localization.

Subcellular location. Nucleus outer membrane. Nucleus envelope. Rough endoplasmic reticulum.

Tissue specificity. Expressed in aortic endothelial cells (at protein level).

Post-translational modifications. The disulfid bond with SUN1 or SUN2 is required for stability of the respective LINC complex under tensile forces.

Domain organisation. The KASH domain is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains.

Similarity. Belongs to the nesprin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6ZMZ3-11, Alphayes
Q6ZMZ3-22
Q6ZMZ3-33

RefSeq proteins (6): NP_001350621, NP_001371210, NP_001371211, NP_001371212, NP_001371213, NP_689805* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002017Spectrin_repeatRepeat
IPR012315KASHDomain
IPR018159Spectrin/alpha-actininRepeat
IPR052403LINC-complex_assocFamily
IPR057932Spectrin_SYNE1_3Domain
IPR057933SYNE3_domDomain

Pfam: PF00435, PF10541, PF25803, PF25804

UniProt features (19 total): sequence variant 5, splice variant 3, topological domain 2, repeat 2, disulfide bond 2, chain 1, strand 1, transmembrane region 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6WMEX-RAY DIFFRACTION1.53

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZMZ3-F180.490.35

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 (2): 953, 953

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 160 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, MYOGENIN_Q6, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, AAGTCCA_MIR422B_MIR422A, BOYLAN_MULTIPLE_MYELOMA_D_DN, BEIER_GLIOMA_STEM_CELL_DN, BILD_HRAS_ONCOGENIC_SIGNATURE, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_NUCLEUS_LOCALIZATION, BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN, SABATES_COLORECTAL_ADENOMA_DN, GOMF_ACTIN_BINDING, CHEN_HOXA5_TARGETS_9HR_DN

GO Biological Process (4): cytoskeleton organization (GO:0007010), nuclear migration (GO:0007097), regulation of cell shape (GO:0008360), establishment of protein localization to membrane (GO:0090150)

GO Molecular Function (3): actin filament binding (GO:0051015), cytoskeleton-nuclear membrane anchor activity (GO:0140444), protein binding (GO:0005515)

GO Cellular Component (9): nuclear envelope (GO:0005635), nuclear outer membrane (GO:0005640), cytoplasm (GO:0005737), rough endoplasmic reticulum (GO:0005791), membrane (GO:0016020), nuclear membrane (GO:0031965), meiotic nuclear membrane microtubule tethering complex (GO:0034993), nucleus (GO:0005634), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nucleus2
endomembrane system2
cellular anatomical structure2
intracellular membrane-bounded organelle2
organelle organization1
intracellular transport1
nucleus localization1
establishment of organelle localization1
regulation of cell morphogenesis1
regulation of biological quality1
establishment of protein localization1
localization within membrane1
actin binding1
protein-containing complex binding1
protein-membrane adaptor activity1
binding1
organelle envelope1
nuclear membrane1
organelle outer membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
intracellular anatomical structure1
endoplasmic reticulum1
nuclear envelope1
organelle membrane1
microtubule organizing center attachment site1
nuclear membrane microtubule tethering complex1
cytoplasm1

Protein interactions and networks

STRING

770 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYNE3PLECQ15149998
SYNE3SYNE4Q8N205916
SYNE3SUN2Q9UH99873
SYNE3MACF1Q9UPN3872
SYNE3SUN1O94901838
SYNE3TOR1AO14656833
SYNE3SUN3Q8TAQ9806
SYNE3ITGB4P16144677
SYNE3KASH5Q8N6L0665
SYNE3SPAG4Q9NPE6636
SYNE3ACTN1P12814590
SYNE3EMDP50402573
SYNE3KRT14P02533563
SYNE3DSTQ03001561
SYNE3SUN5Q8TC36545

IntAct

8 interactions, top by confidence:

ABTypeScore
SUN2SYNE3psi-mi:“MI:0407”(direct interaction)0.560
PRPF40ASYNE3psi-mi:“MI:0915”(physical association)0.400
Ppsi-mi:“MI:0914”(association)0.350
SYNE4SYNE3psi-mi:“MI:0914”(association)0.350
SYNE2SYNE3psi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (447): SYNE3 (Affinity Capture-MS), SYNE3 (Synthetic Lethality), SYNE3 (Protein-RNA), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Affinity Capture-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS), SYNE3 (Proximity Label-MS)

ESM2 similar proteins: A0A8M2BID5, A2CG49, D3ZEY0, D3ZHV2, E9Q557, E9Q8Q6, F1LMV6, F1M0Z1, G3V7L1, O15068, O60229, O60437, O75962, O97592, P02549, P10911, P11277, P11530, P11531, P11532, P11533, P15508, P15924, P30427, P46939, P97924, Q03001, Q0KL02, Q15149, Q1LUA6, Q4FZC9, Q5GN48, Q63406, Q64096, Q6ZMZ3, Q6ZP82, Q6ZWQ0, Q6ZWR6, Q86YR7, Q8NF91

Diamond homologs: Q4FZC9, Q6ZMZ3, Q8WXH0

SIGNOR signaling

2 interactions.

AEffectBMechanism
TP63“up-regulates quantity by expression”SYNE3“transcriptional regulation”
SYNE3“form complex”“LINC complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance166
Likely benign12
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2625 predictions. Top by Δscore:

VariantEffectΔscore
14:95432126:T:Cacceptor_gain1.0000
14:95432126:T:TCacceptor_gain1.0000
14:95433256:CTA:Cdonor_loss1.0000
14:95433258:A:ACdonor_gain1.0000
14:95433259:C:CCdonor_gain1.0000
14:95433259:CCAG:Cdonor_gain1.0000
14:95436805:T:Adonor_gain1.0000
14:95436845:AAGT:Adonor_gain1.0000
14:95436854:G:Cdonor_gain1.0000
14:95439031:A:ACdonor_gain1.0000
14:95439032:C:CCdonor_gain1.0000
14:95439032:CG:Cdonor_gain1.0000
14:95439032:CGCGT:Cdonor_gain1.0000
14:95439606:TCTCA:Tdonor_loss1.0000
14:95439607:CTCA:Cdonor_loss1.0000
14:95439608:TCACC:Tdonor_loss1.0000
14:95439609:CACC:Cdonor_loss1.0000
14:95439610:A:ACdonor_gain1.0000
14:95439610:A:Cdonor_loss1.0000
14:95439611:C:CAdonor_loss1.0000
14:95439611:C:CCdonor_gain1.0000
14:95439611:CCT:Cdonor_gain1.0000
14:95439780:AGCCT:Aacceptor_gain1.0000
14:95439781:GCCT:Gacceptor_gain1.0000
14:95439782:CCTC:Cacceptor_gain1.0000
14:95439783:CT:Cacceptor_gain1.0000
14:95439784:TC:Tacceptor_loss1.0000
14:95439785:C:CCacceptor_gain1.0000
14:95439786:T:Aacceptor_loss1.0000
14:95439793:C:CTacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000014151 (14:95502121 G>A,C), RS1000034442 (14:95424446 C>T), RS1000065368 (14:95487456 C>A,T), RS1000068075 (14:95462411 CT>C), RS1000087195 (14:95502502 C>T), RS1000097405 (14:95466547 C>T), RS1000111424 (14:95429432 G>A), RS1000150038 (14:95477503 C>T), RS1000167107 (14:95429710 C>A,T), RS1000169421 (14:95485612 T>A), RS1000173188 (14:95440558 G>A), RS1000211436 (14:95473182 C>A,T), RS1000241698 (14:95456631 C>A), RS1000249476 (14:95445062 A>G), RS1000262980 (14:95496936 G>A)

Disease associations

OMIM: gene MIM:610861 | 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
GCST001762_336Obesity-related traits8.000000e-06
GCST001901_3Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer3.000000e-07
GCST002805_2Body mass index9.000000e-07
GCST009391_1627Metabolite levels8.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005106body composition measurement
EFO:0005937longitudinal BMI measurement
EFO:0010464beta-aminoisobutyric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs8020368SYNE30.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, increases methylation6
bisphenol Aincreases expression3
Benzo(a)pyreneaffects methylation, decreases expression3
Panobinostatincreases expression, affects cotreatment2
Estradiolaffects binding, increases expression2
Tobacco Smoke Pollutiondecreases expression2
Cyclosporineincreases expression2
GSK-J4decreases expression1
sotorasibaffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
mono-(2-ethylhexyl)phthalateincreases expression1
9,10-dihydro-9,10-dihydroxybenzo(a)pyrenedecreases expression1
N-acetyl-4-benzoquinoneimineaffects response to substance1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
fipronilaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
incobotulinumtoxinAincreases expression1
trametinibaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
NVP-BKM120affects cotreatment, decreases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
DEETaffects cotreatment, decreases 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.