SYNE3
gene geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:19861 |
| Approved symbol | SYNE3 |
| Name | spectrin repeat containing nuclear envelope family member 3 |
| Location | 14q32.13 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ25605, NET53, Nesprin-3, Nesp3 |
| Ensembl gene | ENSG00000176438 |
| Ensembl biotype | protein_coding |
| OMIM | 610861 |
| Entrez | 161176 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001093740 | 95452247 | 95452383 |
| ENSE00001228165 | 95432079 | 95432117 |
| ENSE00001228171 | 95433260 | 95433409 |
| ENSE00001228176 | 95436820 | 95436981 |
| ENSE00001228210 | 95449931 | 95450105 |
| ENSE00001327278 | 95439033 | 95439162 |
| ENSE00001333827 | 95467795 | 95467967 |
| ENSE00001931517 | 95407266 | 95418026 |
| ENSE00003461397 | 95444485 | 95444628 |
| ENSE00003495674 | 95439612 | 95439784 |
| ENSE00003564753 | 95455377 | 95455724 |
| ENSE00003619164 | 95465931 | 95466240 |
| ENSE00003626437 | 95439914 | 95440075 |
| ENSE00003640360 | 95445909 | 95446091 |
| ENSE00003663024 | 95443155 | 95443289 |
| ENSE00003684738 | 95457177 | 95457338 |
| ENSE00003918050 | 95516596 | 95516650 |
| ENSE00003919023 | 95475678 | 95475835 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 144791 | 5.7908 | 1290 |
| 144792 | 0.2013 | 93 |
| 144789 | 0.0993 | 49 |
| 144788 | 0.0878 | 50 |
Top tissues by expression
285 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| tendon of biceps brachii | UBERON:0008188 | 98.61 | gold quality |
| parietal pleura | UBERON:0002400 | 97.73 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 97.30 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 96.82 | gold quality |
| pleura | UBERON:0000977 | 96.55 | gold quality |
| synovial joint | UBERON:0002217 | 96.34 | gold quality |
| skin of hip | UBERON:0001554 | 95.34 | gold quality |
| visceral pleura | UBERON:0002401 | 94.76 | gold quality |
| superficial temporal artery | UBERON:0001614 | 93.70 | gold quality |
| tendon | UBERON:0000043 | 92.77 | gold quality |
| pericardium | UBERON:0002407 | 92.53 | gold quality |
| upper leg skin | UBERON:0004262 | 92.21 | gold quality |
| sural nerve | UBERON:0015488 | 91.80 | gold quality |
| mammary duct | UBERON:0001765 | 91.39 | gold quality |
| tibia | UBERON:0000979 | 90.48 | gold quality |
| periodontal ligament | UBERON:0008266 | 90.17 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 90.04 | gold quality |
| mammary gland | UBERON:0001911 | 89.99 | gold quality |
| calcaneal tendon | UBERON:0003701 | 89.96 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 89.41 | gold quality |
| medial globus pallidus | UBERON:0002477 | 89.11 | gold quality |
| lower lobe of lung | UBERON:0008949 | 88.94 | gold quality |
| upper arm skin | UBERON:0004263 | 88.47 | gold quality |
| connective tissue | UBERON:0002384 | 88.19 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 88.13 | gold quality |
| mammalian vulva | UBERON:0000997 | 88.08 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 88.05 | gold quality |
| adipose tissue | UBERON:0001013 | 87.99 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 87.39 | gold quality |
| globus pallidus | UBERON:0001875 | 87.33 | gold quality |
Single-cell (SCXA)
Detected in 4 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-9067 | yes | 11.89 |
| E-ANND-3 | yes | 7.39 |
| E-MTAB-7303 | no | 210.28 |
| E-MTAB-5061 | no | 3.45 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-568 | 99.98 | 69.86 | 2084 |
| HSA-MIR-548N | 99.98 | 71.94 | 4170 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-MIR-548AP-5P | 99.94 | 71.14 | 3489 |
| HSA-MIR-548J-5P | 99.94 | 71.14 | 3489 |
| HSA-MIR-145-5P | 99.92 | 71.13 | 1836 |
| HSA-MIR-5195-3P | 99.92 | 70.92 | 1877 |
| HSA-MIR-765 | 99.84 | 68.24 | 2442 |
| HSA-MIR-3121-3P | 99.82 | 71.96 | 3630 |
| HSA-MIR-11181-3P | 99.75 | 66.38 | 2205 |
| HSA-MIR-4446-5P | 99.72 | 69.19 | 2544 |
| HSA-MIR-466 | 99.67 | 70.85 | 2863 |
| HSA-MIR-4643 | 99.49 | 67.63 | 1791 |
| HSA-MIR-519D-5P | 99.41 | 69.30 | 2057 |
| HSA-MIR-5683 | 99.36 | 68.59 | 2083 |
| HSA-MIR-3199 | 99.17 | 65.19 | 696 |
| HSA-MIR-8052 | 99.17 | 65.01 | 719 |
| HSA-MIR-4292 | 99.16 | 65.57 | 1767 |
| HSA-MIR-6791-5P | 99.16 | 65.92 | 1844 |
| HSA-MIR-1288-5P | 98.85 | 67.01 | 734 |
| HSA-MIR-3938 | 98.72 | 66.07 | 834 |
| HSA-MIR-3145-5P | 98.57 | 67.83 | 900 |
| HSA-MIR-6827-5P | 98.46 | 64.88 | 1256 |
| HSA-MIR-4443 | 98.02 | 66.25 | 1928 |
| HSA-MIR-6883-3P | 97.97 | 67.35 | 643 |
| HSA-MIR-4305 | 97.94 | 68.63 | 533 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | syne3 | ENSDARG00000023237 |
| mus_musculus | Syne3 | ENSMUSG00000054150 |
| rattus_norvegicus | Syne3 | ENSRNOG00000005287 |
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-3 — Q6ZMZ3 (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 ID | Names | Canonical? |
|---|---|---|
| Q6ZMZ3-1 | 1, Alpha | yes |
| Q6ZMZ3-2 | 2 | |
| Q6ZMZ3-3 | 3 |
RefSeq proteins (6): NP_001350621, NP_001371210, NP_001371211, NP_001371212, NP_001371213, NP_689805* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002017 | Spectrin_repeat | Repeat |
| IPR012315 | KASH | Domain |
| IPR018159 | Spectrin/alpha-actinin | Repeat |
| IPR052403 | LINC-complex_assoc | Family |
| IPR057932 | Spectrin_SYNE1_3 | Domain |
| IPR057933 | SYNE3_dom | Domain |
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.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 6WME | X-RAY DIFFRACTION | 1.53 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q6ZMZ3-F1 | 80.49 | 0.35 |
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:
| Category | Terms |
|---|---|
| nucleus | 2 |
| endomembrane system | 2 |
| cellular anatomical structure | 2 |
| intracellular membrane-bounded organelle | 2 |
| organelle organization | 1 |
| intracellular transport | 1 |
| nucleus localization | 1 |
| establishment of organelle localization | 1 |
| regulation of cell morphogenesis | 1 |
| regulation of biological quality | 1 |
| establishment of protein localization | 1 |
| localization within membrane | 1 |
| actin binding | 1 |
| protein-containing complex binding | 1 |
| protein-membrane adaptor activity | 1 |
| binding | 1 |
| organelle envelope | 1 |
| nuclear membrane | 1 |
| organelle outer membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| intracellular anatomical structure | 1 |
| endoplasmic reticulum | 1 |
| nuclear envelope | 1 |
| organelle membrane | 1 |
| microtubule organizing center attachment site | 1 |
| nuclear membrane microtubule tethering complex | 1 |
| cytoplasm | 1 |
Protein interactions and networks
STRING
770 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SYNE3 | PLEC | Q15149 | 998 |
| SYNE3 | SYNE4 | Q8N205 | 916 |
| SYNE3 | SUN2 | Q9UH99 | 873 |
| SYNE3 | MACF1 | Q9UPN3 | 872 |
| SYNE3 | SUN1 | O94901 | 838 |
| SYNE3 | TOR1A | O14656 | 833 |
| SYNE3 | SUN3 | Q8TAQ9 | 806 |
| SYNE3 | ITGB4 | P16144 | 677 |
| SYNE3 | KASH5 | Q8N6L0 | 665 |
| SYNE3 | SPAG4 | Q9NPE6 | 636 |
| SYNE3 | ACTN1 | P12814 | 590 |
| SYNE3 | EMD | P50402 | 573 |
| SYNE3 | KRT14 | P02533 | 563 |
| SYNE3 | DST | Q03001 | 561 |
| SYNE3 | SUN5 | Q8TC36 | 545 |
IntAct
8 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SUN2 | SYNE3 | psi-mi:“MI:0407”(direct interaction) | 0.560 |
| PRPF40A | SYNE3 | psi-mi:“MI:0915”(physical association) | 0.400 |
| P | psi-mi:“MI:0914”(association) | 0.350 | |
| SYNE4 | SYNE3 | psi-mi:“MI:0914”(association) | 0.350 |
| SYNE2 | SYNE3 | psi-mi:“MI:0914”(association) | 0.350 |
| ATG16L1 | ESYT2 | psi-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.
| A | Effect | B | Mechanism |
|---|---|---|---|
| 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):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 166 |
| Likely benign | 12 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2625 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 14:95432126:T:C | acceptor_gain | 1.0000 |
| 14:95432126:T:TC | acceptor_gain | 1.0000 |
| 14:95433256:CTA:C | donor_loss | 1.0000 |
| 14:95433258:A:AC | donor_gain | 1.0000 |
| 14:95433259:C:CC | donor_gain | 1.0000 |
| 14:95433259:CCAG:C | donor_gain | 1.0000 |
| 14:95436805:T:A | donor_gain | 1.0000 |
| 14:95436845:AAGT:A | donor_gain | 1.0000 |
| 14:95436854:G:C | donor_gain | 1.0000 |
| 14:95439031:A:AC | donor_gain | 1.0000 |
| 14:95439032:C:CC | donor_gain | 1.0000 |
| 14:95439032:CG:C | donor_gain | 1.0000 |
| 14:95439032:CGCGT:C | donor_gain | 1.0000 |
| 14:95439606:TCTCA:T | donor_loss | 1.0000 |
| 14:95439607:CTCA:C | donor_loss | 1.0000 |
| 14:95439608:TCACC:T | donor_loss | 1.0000 |
| 14:95439609:CACC:C | donor_loss | 1.0000 |
| 14:95439610:A:AC | donor_gain | 1.0000 |
| 14:95439610:A:C | donor_loss | 1.0000 |
| 14:95439611:C:CA | donor_loss | 1.0000 |
| 14:95439611:C:CC | donor_gain | 1.0000 |
| 14:95439611:CCT:C | donor_gain | 1.0000 |
| 14:95439780:AGCCT:A | acceptor_gain | 1.0000 |
| 14:95439781:GCCT:G | acceptor_gain | 1.0000 |
| 14:95439782:CCTC:C | acceptor_gain | 1.0000 |
| 14:95439783:CT:C | acceptor_gain | 1.0000 |
| 14:95439784:TC:T | acceptor_loss | 1.0000 |
| 14:95439785:C:CC | acceptor_gain | 1.0000 |
| 14:95439786:T:A | acceptor_loss | 1.0000 |
| 14:95439793:C:CT | acceptor_gain | 1.0000 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST001762_336 | Obesity-related traits | 8.000000e-06 |
| GCST001901_3 | Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer | 3.000000e-07 |
| GCST002805_2 | Body mass index | 9.000000e-07 |
| GCST009391_1627 | Metabolite levels | 8.000000e-06 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005106 | body composition measurement |
| EFO:0005937 | longitudinal BMI measurement |
| EFO:0010464 | beta-aminoisobutyric acid measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs8020368 | SYNE3 | 0.00 | 0 |
CTD chemical–gene interactions
45 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, increases methylation | 6 |
| bisphenol A | increases expression | 3 |
| Benzo(a)pyrene | affects methylation, decreases expression | 3 |
| Panobinostat | increases expression, affects cotreatment | 2 |
| Estradiol | affects binding, increases expression | 2 |
| Tobacco Smoke Pollution | decreases expression | 2 |
| Cyclosporine | increases expression | 2 |
| GSK-J4 | decreases expression | 1 |
| sotorasib | affects cotreatment, decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| mono-(2-ethylhexyl)phthalate | increases expression | 1 |
| 9,10-dihydro-9,10-dihydroxybenzo(a)pyrene | decreases expression | 1 |
| N-acetyl-4-benzoquinoneimine | affects response to substance | 1 |
| aflatoxin B2 | increases methylation | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects cotreatment, decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| fipronil | affects cotreatment, decreases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| 2,2’,4,4’,5-brominated diphenyl ether | increases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| incobotulinumtoxinA | increases expression | 1 |
| trametinib | affects cotreatment, decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| NVP-BKM120 | affects cotreatment, decreases expression | 1 |
| Temozolomide | decreases expression | 1 |
| Sunitinib | increases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Arsenic | affects methylation | 1 |
| DEET | affects cotreatment, decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.