NSG1
gene geneOn this page
Also known as P21D4S234ENEEP21
Summary
NSG1 (neuronal vesicle trafficking associated 1, HGNC:18790) is a protein-coding gene on chromosome 4p16.3, encoding Neuronal vesicle trafficking-associated protein 1 (P42857). Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway.
Predicted to enable clathrin light chain binding activity. Involved in apoptotic process. Located in endoplasmic reticulum.
Source: NCBI Gene 27065 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 7 total
- MANE Select transcript:
NM_014392
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:18790 |
| Approved symbol | NSG1 |
| Name | neuronal vesicle trafficking associated 1 |
| Location | 4p16.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | P21, D4S234E, NEEP21 |
| Ensembl gene | ENSG00000168824 |
| Ensembl biotype | protein_coding |
| OMIM | 607645 |
| Entrez | 27065 |
Gene structure
Transcript identifiers
Ensembl transcripts: 19 — 16 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay
ENST00000397958, ENST00000421177, ENST00000433139, ENST00000450293, ENST00000504171, ENST00000504347, ENST00000505246, ENST00000506380, ENST00000513555, ENST00000513829, ENST00000621129, ENST00000889808, ENST00000889809, ENST00000889810, ENST00000930399, ENST00000930400, ENST00000930401, ENST00000930402, ENST00000963790
RefSeq mRNA: 6 — MANE Select: NM_014392
NM_001040101, NM_001287763, NM_001287764, NM_001382227, NM_001382228, NM_014392
CCDS: CCDS3376, CCDS93472
Canonical transcript exons
ENST00000621129 — 5 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001161904 | 4409573 | 4409683 |
| ENSE00001161909 | 4391475 | 4391591 |
| ENSE00001161930 | 4387604 | 4387758 |
| ENSE00001704112 | 4417235 | 4419058 |
| ENSE00003933910 | 4387102 | 4387173 |
Expression profiles
Bgee: expression breadth ubiquitous, 260 present calls, max score 99.52.
FANTOM5 (CAGE): breadth broad, TPM avg 14.8437 / max 445.2521, expressed in 766 samples.
FANTOM5 promoters (9 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 46742 | 9.4468 | 694 |
| 46735 | 3.3339 | 475 |
| 46734 | 0.6123 | 230 |
| 46737 | 0.4548 | 196 |
| 46738 | 0.2999 | 159 |
| 46740 | 0.2225 | 117 |
| 46741 | 0.1880 | 99 |
| 46739 | 0.1840 | 106 |
| 46736 | 0.1016 | 55 |
Top tissues by expression
286 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| secondary oocyte | CL:0000655 | 99.52 | gold quality |
| cortical plate | UBERON:0005343 | 99.48 | gold quality |
| endothelial cell | CL:0000115 | 99.30 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 99.22 | gold quality |
| ganglionic eminence | UBERON:0004023 | 98.69 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 98.52 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 98.41 | gold quality |
| pons | UBERON:0000988 | 98.39 | gold quality |
| oocyte | CL:0000023 | 97.92 | gold quality |
| pituitary gland | UBERON:0000007 | 97.70 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 97.29 | gold quality |
| adenohypophysis | UBERON:0002196 | 96.95 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 96.92 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 96.76 | gold quality |
| cerebellar cortex | UBERON:0002129 | 96.29 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 96.28 | gold quality |
| cerebellum | UBERON:0002037 | 96.04 | gold quality |
| gingival epithelium | UBERON:0001949 | 95.70 | gold quality |
| skin of leg | UBERON:0001511 | 95.57 | gold quality |
| gingiva | UBERON:0001828 | 95.57 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 95.53 | gold quality |
| hypothalamus | UBERON:0001898 | 95.49 | gold quality |
| skin of abdomen | UBERON:0001416 | 95.39 | gold quality |
| primary visual cortex | UBERON:0002436 | 95.36 | gold quality |
| nucleus accumbens | UBERON:0001882 | 95.12 | gold quality |
| zone of skin | UBERON:0000014 | 95.02 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 94.99 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 94.83 | gold quality |
| embryo | UBERON:0000922 | 94.51 | gold quality |
| right frontal lobe | UBERON:0002810 | 94.37 | gold quality |
Single-cell (SCXA)
Detected in 11 experiment(s), a significant marker in 9.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-9906 | yes | 734.23 |
| E-ANND-5 | yes | 599.27 |
| E-GEOD-93593 | yes | 590.04 |
| E-HCAD-5 | yes | 48.48 |
| E-MTAB-8142 | yes | 19.03 |
| E-GEOD-137537 | yes | 15.04 |
| E-HCAD-25 | yes | 11.93 |
| E-MTAB-5061 | yes | 11.28 |
| E-ANND-3 | yes | 10.98 |
| E-MTAB-9154 | no | 1073.88 |
| E-ENAD-20 | no | 579.40 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
129 targeting NSG1, 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-30A-5P | 100.00 | 76.31 | 3233 |
| HSA-MIR-30B-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30C-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30D-5P | 100.00 | 76.32 | 3233 |
| HSA-MIR-30E-5P | 100.00 | 76.32 | 3242 |
| HSA-MIR-188-3P | 100.00 | 68.76 | 1240 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-4283 | 100.00 | 66.42 | 2097 |
| HSA-MIR-8485 | 100.00 | 77.57 | 4731 |
| HSA-MIR-3064-3P | 100.00 | 70.09 | 1254 |
| HSA-MIR-181A-5P | 99.99 | 72.96 | 2995 |
| HSA-MIR-181B-5P | 99.99 | 72.97 | 2996 |
| HSA-MIR-181C-5P | 99.99 | 72.95 | 2996 |
| HSA-MIR-181D-5P | 99.99 | 73.04 | 2997 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-103A-3P | 99.98 | 69.14 | 1595 |
| HSA-MIR-107 | 99.98 | 69.14 | 1595 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-4482-3P | 99.98 | 72.50 | 3147 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-27A-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-27B-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-9985 | 99.98 | 72.11 | 2939 |
| HSA-MIR-4803 | 99.98 | 71.99 | 3117 |
| HSA-MIR-25-3P | 99.98 | 74.60 | 1817 |
| HSA-MIR-32-5P | 99.98 | 75.21 | 1964 |
Literature-anchored findings (GeneRIF, showing 5)
- a novel p53-responsive gene D4S234E is accumulated in the ER and induces apoptosis in response to DNA damage. (PMID:20599942)
- These results suggest that NEEP21 may play a critical role in apoptosis as a mediator of p53. (PMID:20878061)
- NEEP21 profoundly affects the processing of beta-amyloid precursor proteins and Abeta peptide production. (PMID:21084623)
- This review focuses on two closely related, neuron-enriched endosomal proteins: NEEP21 and Calcyon which perform distinct roles in regulating receptor endocytosis, recycling, and degradation–{REVIEW} (PMID:25376768)
- miR-107 Targets NSG1 to Regulate Hypopharyngeal Squamous Cell Carcinoma Progression through ERK Pathway. (PMID:38892156)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Nsg1 | ENSMUSG00000029126 |
| rattus_norvegicus | Nsg1 | ENSRNOG00000005700 |
Paralogs (2): CALY (ENSG00000130643), NSG2 (ENSG00000170091)
Protein
Protein identifiers
Neuronal vesicle trafficking-associated protein 1 — P42857 (reviewed: P42857)
Alternative names: Neuron-enriched endosomal protein of 21 kDa, Neuron-specific protein family member 1
All UniProt accessions (2): P42857, B2R5R8
UniProt curated annotations — full annotation on UniProt →
Function. Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway. Regulates sorting and recycling of GRIA2 through interaction with GRIP1 and then contributes to the regulation of synaptic transmission and plasticity by affecting the recycling and targeting of AMPA receptors to the synapse. Is required for faithful sorting of L1CAM to axons by facilitating trafficking from somatodendritic early endosome or the recycling endosome. In an other hand, induces apoptosis via the activation of CASP3 in response to DNA damage.
Subunit / interactions. Forms a complex with GRIP1, GRIA2 and STX12 through direct interaction with GRIP1; controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting. Interacts with STX12. Interacts with APP; could regulate APP processing. Interacts with FAM171A1.
Subcellular location. Membrane. Golgi apparatus. trans-Golgi network membrane. Endosome membrane. Cell projection. Dendrite. Early endosome membrane. Late endosome membrane. Lysosome lumen. Recycling endosome membrane. Cytoplasmic vesicle membrane. Golgi stack membrane. Endosome. Multivesicular body membrane. Endoplasmic reticulum membrane.
Induction. Up-regulated by TP53 after DNA damage. Up-regulated by genotoxic stress.
Similarity. Belongs to the NSG family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| P42857-1 | 1 | yes |
| P42857-2 | 2 |
RefSeq proteins (6): NP_001035190, NP_001274692, NP_001274693, NP_001369156, NP_001369157, NP_055207* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR009431 | NSG | Family |
Pfam: PF06387
UniProt features (6 total): topological domain 2, chain 1, transmembrane region 1, region of interest 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P42857-F1 | 60.70 | 0.08 |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 252 (showing top):
GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_CLATHRIN_COAT_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, BAKER_HEMATOPOESIS_STAT1_TARGETS, BAKER_HEMATOPOIESIS_STAT3_TARGETS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP, GOBP_CELL_CELL_SIGNALING, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, GOCC_TRANS_GOLGI_NETWORK, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, MODULE_379, BILD_E2F3_ONCOGENIC_SIGNATURE, HUPER_BREAST_BASAL_VS_LUMINAL_UP
GO Biological Process (12): receptor recycling (GO:0001881), positive regulation of receptor recycling (GO:0001921), apoptotic process (GO:0006915), endosomal transport (GO:0016197), amyloid precursor protein metabolic process (GO:0042982), clathrin coat assembly (GO:0048268), spontaneous synaptic transmission (GO:0098814), neurotransmitter receptor transport, endosome to postsynaptic membrane (GO:0098887), vesicle-mediated transport in synapse (GO:0099003), neurotransmitter receptor cycle (GO:0099627), postsynaptic neurotransmitter receptor cycle (GO:0099630), regulation of long-term synaptic potentiation (GO:1900271)
GO Molecular Function (4): clathrin light chain binding (GO:0032051), ionotropic glutamate receptor binding (GO:0035255), signaling receptor binding (GO:0005102), protein binding (GO:0005515)
GO Cellular Component (27): nucleus (GO:0005634), cytoplasm (GO:0005737), endosome (GO:0005768), late endosome (GO:0005770), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), lateral plasma membrane (GO:0016328), dendrite (GO:0030425), early endosome membrane (GO:0031901), Golgi cisterna membrane (GO:0032580), multivesicular body membrane (GO:0032585), trans-Golgi network membrane (GO:0032588), somatodendritic compartment (GO:0036477), lysosomal lumen (GO:0043202), postsynaptic membrane (GO:0045211), recycling endosome membrane (GO:0055038), postsynaptic endosome (GO:0098845), glutamatergic synapse (GO:0098978), lysosome (GO:0005764), early endosome (GO:0005769), Golgi apparatus (GO:0005794), endosome membrane (GO:0010008), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), late endosome membrane (GO:0031902), cell projection (GO:0042995)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 4 |
| postsynapse | 3 |
| organelle membrane | 3 |
| vesicle-mediated transport | 2 |
| synapse | 2 |
| intracellular membrane-bounded organelle | 2 |
| endomembrane system | 2 |
| endosome | 2 |
| endosome membrane | 2 |
| endocytosis | 1 |
| receptor metabolic process | 1 |
| receptor recycling | 1 |
| regulation of receptor recycling | 1 |
| positive regulation of macromolecule metabolic process | 1 |
| positive regulation of signaling | 1 |
| programmed cell death | 1 |
| apoptotic signaling pathway | 1 |
| execution phase of apoptosis | 1 |
| intracellular transport | 1 |
| protein metabolic process | 1 |
| protein-containing complex assembly | 1 |
| chemical synaptic transmission | 1 |
| spontaneous neurotransmitter secretion | 1 |
| intercellular transport | 1 |
| neurotransmitter receptor transport to postsynaptic membrane | 1 |
| neurotransmitter receptor transport, endosome to plasma membrane | 1 |
| neurotransmitter receptor transport | 1 |
| establishment of localization in cell | 1 |
| neurotransmitter receptor cycle | 1 |
| regulation of synaptic plasticity | 1 |
| long-term synaptic potentiation | 1 |
| clathrin binding | 1 |
| glutamate receptor binding | 1 |
| protein binding | 1 |
| binding | 1 |
| intracellular anatomical structure | 1 |
| cytoplasmic vesicle | 1 |
| cytoplasm | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
Protein interactions and networks
STRING
642 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| NSG1 | STX18 | Q9P2W9 | 806 |
| NSG1 | GRIP1 | Q9Y3R0 | 783 |
| NSG1 | EVC2 | Q86UK5 | 749 |
| NSG1 | CRMP1 | Q14194 | 717 |
| NSG1 | EVC | P57679 | 639 |
| NSG1 | GRIA2 | P42262 | 621 |
| NSG1 | GRIA1 | P42261 | 571 |
| NSG1 | MSX1 | P28360 | 557 |
| NSG1 | GRIPAP1 | Q4V328 | 502 |
| NSG1 | PICK1 | Q9NRD5 | 495 |
| NSG1 | OAZ1 | P54368 | 442 |
| NSG1 | STX12 | Q86Y82 | 440 |
| NSG1 | CENPH | Q9H3R5 | 419 |
| NSG1 | SRSF5 | Q13243 | 403 |
| NSG1 | EEIG2 | Q5T8I3 | 394 |
| NSG1 | TMEM128 | Q5BJH2 | 394 |
IntAct
120 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| NSG1 | KASH5 | psi-mi:“MI:0915”(physical association) | 0.720 |
| KASH5 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.720 |
| NSG1 | BSCL2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| BSCL2 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | TMEM139 | psi-mi:“MI:0915”(physical association) | 0.560 |
| OPRM1 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| NSG1 | CREB3L1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | FNDC9 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | SLC7A14 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SLC30A4 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | SPACA1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | TMEM207 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | TMEM52B | psi-mi:“MI:0915”(physical association) | 0.560 |
| ATP6AP2 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | KIR2DL3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | PDZK1IP1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| EVI2B | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FFAR2 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FCGR2A | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | RELL2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | TMX2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| MGST3 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NSG1 | BTN2A1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| GPR42 | NSG1 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (43): NSG1 (Two-hybrid), CCDC155 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid)
ESM2 similar proteins: A4IG66, B2RUZ4, B3DHH5, F1NVK6, F1Q930, O70367, O76024, O77770, O95772, P02683, P0C8K7, P42857, P56695, P84889, Q0P4Z1, Q15053, Q1JPG0, Q28DG6, Q2TBG9, Q4QQM5, Q4R5Q3, Q56JY4, Q5BLE2, Q5M836, Q5RF46, Q5XJS0, Q5ZKK0, Q62092, Q6GR21, Q6IQA2, Q6NRB7, Q6P606, Q7L4E1, Q7Z3D4, Q8BG50, Q8BK03, Q8BXV2, Q8IUW5, Q8K2J7, Q8NAN2
Diamond homologs: P02683, P42857, P47759, P58821, Q0VCZ0, Q3KR51, Q4R5Q3, Q5RF46, Q62092, Q8QFP1, Q9DCA7, Q9NYX4, Q9Y328
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
7 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 5 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1935 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 4:4387759:G:GA | donor_loss | 1.0000 |
| 4:4387759:G:GG | donor_gain | 1.0000 |
| 4:4387760:T:G | donor_loss | 1.0000 |
| 4:4391460:T:TA | acceptor_gain | 1.0000 |
| 4:4391467:T:A | acceptor_gain | 1.0000 |
| 4:4391468:G:A | acceptor_gain | 1.0000 |
| 4:4391471:TAAG:T | acceptor_loss | 1.0000 |
| 4:4391472:A:AG | acceptor_gain | 1.0000 |
| 4:4391472:AAG:A | acceptor_gain | 1.0000 |
| 4:4391472:AAGGT:A | acceptor_gain | 1.0000 |
| 4:4391473:A:G | acceptor_gain | 1.0000 |
| 4:4391473:AGGT:A | acceptor_gain | 1.0000 |
| 4:4391474:G:A | acceptor_gain | 1.0000 |
| 4:4391474:G:GC | acceptor_loss | 1.0000 |
| 4:4391474:GGTG:G | acceptor_gain | 1.0000 |
| 4:4391586:TTTA:T | donor_gain | 1.0000 |
| 4:4391589:AAG:A | donor_loss | 1.0000 |
| 4:4391592:GTG:G | donor_loss | 1.0000 |
| 4:4391593:T:G | donor_loss | 1.0000 |
| 4:4409567:CCACA:C | acceptor_loss | 1.0000 |
| 4:4409568:CACAG:C | acceptor_loss | 1.0000 |
| 4:4409570:CA:C | acceptor_loss | 1.0000 |
| 4:4409571:A:AG | acceptor_gain | 1.0000 |
| 4:4409571:A:C | acceptor_loss | 1.0000 |
| 4:4409572:G:GT | acceptor_gain | 1.0000 |
| 4:4409572:GGTCT:G | acceptor_gain | 1.0000 |
| 4:4409640:TGTAC:T | donor_gain | 1.0000 |
| 4:4409681:AAG:A | donor_loss | 1.0000 |
| 4:4409684:GT:G | donor_loss | 1.0000 |
| 4:4409685:T:A | donor_loss | 1.0000 |
AlphaMissense
1204 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 4:4409612:T:C | C96R | 0.999 |
| 4:4409660:T:C | C112R | 0.998 |
| 4:4417244:T:A | C123S | 0.998 |
| 4:4417244:T:C | C123R | 0.998 |
| 4:4417245:G:C | C123S | 0.998 |
| 4:4387721:T:A | L31H | 0.997 |
| 4:4409595:C:A | A90D | 0.997 |
| 4:4409616:T:A | V97D | 0.997 |
| 4:4409607:T:C | L94P | 0.996 |
| 4:4409660:T:A | C112S | 0.996 |
| 4:4409661:G:C | C112S | 0.996 |
| 4:4387736:T:C | L36P | 0.995 |
| 4:4409607:T:A | L94H | 0.995 |
| 4:4409607:T:G | L94R | 0.995 |
| 4:4409661:G:A | C112Y | 0.995 |
| 4:4409662:C:G | C112W | 0.995 |
| 4:4417246:C:G | C123W | 0.995 |
| 4:4409586:T:A | V87D | 0.994 |
| 4:4409625:T:C | L100P | 0.994 |
| 4:4409628:T:A | V101D | 0.994 |
| 4:4409672:T:C | F116L | 0.994 |
| 4:4409674:C:A | F116L | 0.994 |
| 4:4409674:C:G | F116L | 0.994 |
| 4:4387693:T:C | F22L | 0.993 |
| 4:4387695:C:A | F22L | 0.993 |
| 4:4387695:C:G | F22L | 0.993 |
| 4:4387721:T:C | L31P | 0.993 |
| 4:4409598:T:C | L91P | 0.993 |
| 4:4409598:T:G | L91R | 0.993 |
| 4:4387709:T:C | L27P | 0.992 |
dbSNP variants (sampled 300 via entrez): RS1000101417 (4:4416706 C>G), RS10002237 (4:4417884 C>T), RS1000245748 (4:4400245 C>T), RS1000310322 (4:4411054 C>T), RS1000457234 (4:4394648 A>T), RS1000506951 (4:4397652 G>A,C), RS1000527789 (4:4398947 T>A), RS1000580248 (4:4398726 G>A), RS1000676336 (4:4386701 G>A,T), RS1000810713 (4:4414633 C>A,T), RS1000839739 (4:4408324 T>A), RS10008550 (4:4384861 C>G,T), RS1000870988 (4:4408098 T>C), RS1000937479 (4:4386912 C>A,T), RS1001033624 (4:4409951 C>T)
Disease associations
OMIM: gene MIM:607645 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST005173_80 | Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes | 3.000000e-07 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004723 | coronary artery calcification |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
39 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, affects expression | 8 |
| Benzo(a)pyrene | affects methylation, increases expression | 2 |
| Diethylhexyl Phthalate | decreases methylation, increases abundance, decreases expression | 2 |
| Doxorubicin | increases expression | 2 |
| Estradiol | affects cotreatment, increases expression | 2 |
| Aflatoxin B1 | decreases expression, increases methylation | 2 |
| methylmercuric chloride | decreases expression | 1 |
| triphenyl phosphate | decreases expression | 1 |
| propionaldehyde | increases expression | 1 |
| testosterone undecanoate | affects cotreatment, decreases expression | 1 |
| trichostatin A | increases expression | 1 |
| mono-(2-ethylhexyl)phthalate | decreases methylation, increases abundance | 1 |
| butyraldehyde | increases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| beta-methylcholine | affects expression | 1 |
| pentanal | increases expression | 1 |
| deguelin | decreases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | increases expression, affects cotreatment | 1 |
| nutlin 3 | affects cotreatment, increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Air Pollutants | increases abundance, increases expression | 1 |
| Aldehydes | increases expression | 1 |
| Camptothecin | increases expression | 1 |
| Cisplatin | affects cotreatment, increases expression | 1 |
| Dactinomycin | affects cotreatment, increases expression | 1 |
| Formaldehyde | decreases expression | 1 |
| Methapyrilene | increases methylation | 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.