RETREG3
geneOn this page
Also known as DKFZp686B1036FLJ33806
Summary
RETREG3 (reticulophagy regulator family member 3, HGNC:27258) is a protein-coding gene on chromosome 17q21.2, encoding Reticulophagy regulator 3 (Q86VR2). Endoplasmic reticulum (ER)-anchored autophagy regulator which exists in an inactive state under basal conditions but is activated following cellular stress.
Predicted to enable endoplasmic reticulum-autophagosome adaptor activity. Involved in endoplasmic reticulum tubular network organization; positive regulation of neuron projection development; and reticulophagy. Located in endoplasmic reticulum tubular network. Part of protein-containing complex.
Source: NCBI Gene 162427 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 78 total — 1 likely-pathogenic
- MANE Select transcript:
NM_178126
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:27258 |
| Approved symbol | RETREG3 |
| Name | reticulophagy regulator family member 3 |
| Location | 17q21.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | DKFZp686B1036, FLJ33806 |
| Ensembl gene | ENSG00000141699 |
| Ensembl biotype | protein_coding |
| OMIM | 616498 |
| Entrez | 162427 |
Gene structure
Transcript identifiers
Ensembl transcripts: 16 — 8 protein_coding, 5 nonsense_mediated_decay, 3 retained_intron
ENST00000309428, ENST00000585726, ENST00000585894, ENST00000586796, ENST00000586870, ENST00000588423, ENST00000589007, ENST00000589797, ENST00000590035, ENST00000590541, ENST00000591547, ENST00000593251, ENST00000875457, ENST00000875458, ENST00000917259, ENST00000955309
RefSeq mRNA: 1 — MANE Select: NM_178126
NM_178126
CCDS: CCDS11432
Canonical transcript exons
ENST00000309428 — 9 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001320492 | 42587834 | 42587864 |
| ENSE00002875077 | 42579515 | 42582270 |
| ENSE00003469683 | 42582674 | 42582806 |
| ENSE00003472314 | 42592056 | 42592162 |
| ENSE00003519199 | 42586765 | 42586891 |
| ENSE00003565339 | 42585125 | 42585262 |
| ENSE00003565827 | 42583498 | 42583580 |
| ENSE00003613741 | 42586053 | 42586137 |
| ENSE00003850199 | 42609086 | 42609374 |
Expression profiles
Bgee: expression breadth ubiquitous, 295 present calls, max score 96.41.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.1876 / max 215.6569, expressed in 1817 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 166172 | 22.1876 | 1817 |
Top tissues by expression
300 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 96.41 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 95.58 | gold quality |
| nasopharynx | UBERON:0001728 | 95.56 | gold quality |
| gingival epithelium | UBERON:0001949 | 95.43 | gold quality |
| nipple | UBERON:0002030 | 95.20 | gold quality |
| periodontal ligament | UBERON:0008266 | 94.88 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 94.66 | gold quality |
| gingiva | UBERON:0001828 | 94.37 | gold quality |
| pylorus | UBERON:0001166 | 94.16 | gold quality |
| body of pancreas | UBERON:0001150 | 94.15 | gold quality |
| granulocyte | CL:0000094 | 93.95 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 93.88 | gold quality |
| ileal mucosa | UBERON:0000331 | 93.83 | gold quality |
| thymus | UBERON:0002370 | 93.71 | gold quality |
| right testis | UBERON:0004534 | 93.70 | gold quality |
| left testis | UBERON:0004533 | 93.57 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 93.48 | gold quality |
| superior surface of tongue | UBERON:0007371 | 93.48 | gold quality |
| mammary duct | UBERON:0001765 | 93.40 | gold quality |
| upper leg skin | UBERON:0004262 | 93.38 | gold quality |
| penis | UBERON:0000989 | 93.36 | gold quality |
| upper arm skin | UBERON:0004263 | 93.35 | gold quality |
| trachea | UBERON:0003126 | 93.04 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 92.93 | gold quality |
| mammalian vulva | UBERON:0000997 | 92.89 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 92.70 | gold quality |
| blood | UBERON:0000178 | 92.66 | gold quality |
| cardia of stomach | UBERON:0001162 | 92.64 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 92.61 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 92.59 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 7.55 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): NRF1
miRNA regulators (miRDB)
181 targeting RETREG3, 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-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-12118 | 100.00 | 65.88 | 1270 |
| HSA-MIR-4533 | 100.00 | 69.48 | 2758 |
| HSA-MIR-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-5193 | 100.00 | 67.26 | 1744 |
| HSA-MIR-4476 | 100.00 | 68.18 | 2030 |
| HSA-MIR-6876-5P | 100.00 | 67.68 | 2126 |
| HSA-MIR-6758-5P | 100.00 | 66.21 | 1470 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-6870-5P | 99.99 | 68.55 | 2115 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-150-5P | 99.99 | 66.69 | 1976 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-513B-5P | 99.99 | 69.96 | 2150 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-3173-3P | 99.98 | 66.49 | 1217 |
| HSA-MIR-6891-5P | 99.98 | 66.53 | 1372 |
| HSA-MIR-3617-3P | 99.98 | 67.86 | 918 |
| 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-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-485-3P | 99.98 | 70.68 | 1585 |
| HSA-MIR-539-3P | 99.98 | 70.74 | 1616 |
| HSA-MIR-4723-5P | 99.97 | 68.70 | 2034 |
| HSA-MIR-5698 | 99.97 | 68.49 | 2029 |
| HSA-MIR-7111-5P | 99.97 | 68.48 | 2062 |
| HSA-MIR-302E | 99.96 | 70.74 | 2669 |
| HSA-MIR-6778-3P | 99.96 | 67.29 | 2693 |
Literature-anchored findings (GeneRIF, showing 2)
- We verified that NRF-1 positively regulates FAM134C and ENOX1, and negatively regulates C3orf10 in human neuroblastoma IMR-32 cells and primary rat cortical neurons. (PMID:23939472)
- RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy. (PMID:33826365)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Retreg3 | ENSMUSG00000017802 |
| rattus_norvegicus | Retreg3 | ENSRNOG00000020056 |
Protein
Protein identifiers
Reticulophagy regulator 3 — Q86VR2 (reviewed: Q86VR2)
All UniProt accessions (9): Q86VR2, K7EJ34, K7EJ42, K7ELM8, K7EMF4, K7ENF4, K7ENZ6, K7EPD0, K7EQI9
UniProt curated annotations — full annotation on UniProt →
Function. Endoplasmic reticulum (ER)-anchored autophagy regulator which exists in an inactive state under basal conditions but is activated following cellular stress. When activated, induces ER fragmentation and mediates ER delivery into lysosomes through sequestration into autophagosomes via interaction with ATG8 family proteins. Promotes ER membrane curvature and ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes. Required for collagen quality control in a LIR motif-dependent manner. Mediates NRF1-enhanced neurite outgrowth.
Subunit / interactions. Interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1 and GABARAPL2. Interacts with CANX. Interacts with RTN4 isoform B.
Subcellular location. Endoplasmic reticulum membrane.
Domain organisation. The LIR motif interacts with ATG8 family proteins.
Induction. Induced by amino acid starvation but not by endoplasmic reticulum stress.
Similarity. Belongs to the RETREG family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q86VR2-1 | 1 | yes |
| Q86VR2-2 | 2 |
RefSeq proteins (1): NP_835227* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR043384 | RETREG1/3 | Family |
| IPR055258 | RETR3_RHD | Domain |
| IPR057282 | RETREG1-3-like_RHD | Domain |
Pfam: PF24456
UniProt features (38 total): modified residue 16, topological domain 5, compositionally biased region 4, transmembrane region 4, region of interest 3, mutagenesis site 2, initiator methionine 1, chain 1, short sequence motif 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q86VR2-F1 | 61.61 | 0.00 |
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 (16): 2, 10, 26, 258, 260, 283, 285, 288, 293, 303, 307, 310, 313, 320, 360, 440
Mutagenesis-validated functional residues (2):
| Position | Phenotype |
|---|---|
| 445–450 | reduced formation of autophagosomes. |
| 447–450 | abolishes interaction with atg8 family proteins, induction of er fragmentation and er degradation. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 195 (showing top):
AAGCAAT_MIR137, TGCGCANK_UNKNOWN, GOBP_VACUOLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_NEUROGENESIS, GOBP_MACROAUTOPHAGY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, MARTINEZ_RB1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_ORGANELLE_ASSEMBLY, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, DOUGLAS_BMI1_TARGETS_DN, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_ENDOPLASMIC_RETICULUM_ORGANIZATION
GO Biological Process (7): positive regulation of neuron projection development (GO:0010976), collagen catabolic process (GO:0030574), reticulophagy (GO:0061709), endoplasmic reticulum tubular network organization (GO:0071786), autophagy (GO:0006914), endoplasmic reticulum organization (GO:0007029), substrate localization to autophagosome (GO:0061753)
GO Molecular Function (2): endoplasmic reticulum-autophagosome adaptor activity (GO:0140506), protein binding (GO:0005515)
GO Cellular Component (5): endoplasmic reticulum membrane (GO:0005789), protein-containing complex (GO:0032991), endoplasmic reticulum tubular network (GO:0071782), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| catabolic process | 2 |
| endoplasmic reticulum subcompartment | 2 |
| regulation of neuron projection development | 1 |
| neuron projection development | 1 |
| positive regulation of cell projection organization | 1 |
| collagen metabolic process | 1 |
| macroautophagy | 1 |
| endoplasmic reticulum organization | 1 |
| transmembrane transport | 1 |
| process utilizing autophagic mechanism | 1 |
| organelle organization | 1 |
| endomembrane system organization | 1 |
| autophagosome assembly | 1 |
| establishment of localization in cell | 1 |
| autophagosome-membrane adaptor activity | 1 |
| endoplasmic reticulum-organelle membrane tether activity | 1 |
| binding | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| cellular_component | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
1430 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| RETREG3 | GABARAP | O95166 | 793 |
| RETREG3 | TEX264 | Q9Y6I9 | 548 |
| RETREG3 | CCPG1 | Q9ULG6 | 537 |
| RETREG3 | MANSC1 | Q9H8J5 | 522 |
| RETREG3 | TMEM171 | Q8WVE6 | 502 |
| RETREG3 | RTN3 | O95197 | 495 |
| RETREG3 | SEC62 | Q99442 | 493 |
| RETREG3 | LNPK | Q9C0E8 | 450 |
| RETREG3 | RTN4 | Q9NQC3 | 413 |
| RETREG3 | ENOX1 | Q8TC92 | 405 |
| RETREG3 | CACFD1 | Q9UGQ2 | 404 |
| RETREG3 | MRFAP1L1 | Q96HT8 | 402 |
| RETREG3 | PACC1 | Q9H813 | 399 |
| RETREG3 | ENTREP1 | Q15884 | 386 |
| RETREG3 | ATL3 | Q6DD88 | 380 |
IntAct
488 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| RETREG3 | GABARAPL1 | psi-mi:“MI:0915”(physical association) | 0.830 |
| GABARAPL1 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.830 |
| ABHD16A | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.780 |
| ARL6IP1 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.780 |
| RETREG3 | MAP1LC3A | psi-mi:“MI:0915”(physical association) | 0.780 |
| RETREG3 | ABHD16A | psi-mi:“MI:0915”(physical association) | 0.780 |
| RETREG3 | ARL6IP1 | psi-mi:“MI:0915”(physical association) | 0.780 |
| MAP1LC3A | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.780 |
| RETREG3 | STAP1 | psi-mi:“MI:0915”(physical association) | 0.720 |
| ATP5PB | SLC19A2 | psi-mi:“MI:0914”(association) | 0.640 |
| CCDC167 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LRCH4 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| MOB2 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TMEM65 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CMTM3 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| YIPF1 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CMTM5 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HMOX2 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ANKRD46 | RETREG3 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (341): FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Affinity Capture-RNA), FAM134C (Affinity Capture-RNA), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), JPH1 (Affinity Capture-MS), ATP12A (Affinity Capture-MS)
ESM2 similar proteins: A1L3T7, A2A699, A7YWL5, O70622, O75298, O94983, Q0P4Z1, Q16799, Q1L899, Q1LU99, Q2T9L4, Q3T1H8, Q3TES0, Q3UJB9, Q3ZAV8, Q4FZU8, Q4VAC9, Q5E9U3, Q5IS59, Q5RBI7, Q5XIS1, Q64548, Q66H43, Q68FE6, Q6NS82, Q6P2E9, Q6PDH0, Q6WN19, Q6ZQ29, Q6ZS17, Q76LL6, Q76N89, Q80Y50, Q86UU1, Q86VR2, Q8BG26, Q8CD60, Q8K0T0, Q8K330, Q8TE77
Diamond homologs: Q0P4Z1, Q3MHU5, Q5E9K8, Q5FVM3, Q6NS82, Q86VR2, Q8NC44, Q8VE91, Q9CQV4, Q9H6L5
SIGNOR signaling
3 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| NRF1 | “up-regulates quantity by expression” | RETREG3 | “transcriptional regulation” |
| NRF1 | up-regulates | RETREG3 | |
| RETREG3 | up-regulates | Neurite_outgrowth |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 125 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.
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| vesicle fusion | 5 | 30.7× | 1e-04 |
| endoplasmic reticulum organization | 5 | 21.5× | 6e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
78 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 1 |
| Uncertain significance | 67 |
| Likely benign | 1 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3338057 | NM_001070.5(TUBG1):c.664A>C (p.Asn222His) | Likely pathogenic |
SpliceAI
2050 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 17:42582266:TAGGT:T | acceptor_gain | 1.0000 |
| 17:42582270:TC:T | acceptor_loss | 1.0000 |
| 17:42582271:C:CC | acceptor_gain | 1.0000 |
| 17:42582668:CCTCA:C | donor_loss | 1.0000 |
| 17:42582669:CTCAC:C | donor_loss | 1.0000 |
| 17:42582670:TCACC:T | donor_loss | 1.0000 |
| 17:42582671:CA:C | donor_loss | 1.0000 |
| 17:42582673:C:CG | donor_loss | 1.0000 |
| 17:42582685:T:TA | donor_gain | 1.0000 |
| 17:42582803:CCAG:C | acceptor_gain | 1.0000 |
| 17:42582804:CAG:C | acceptor_gain | 1.0000 |
| 17:42582804:CAGC:C | acceptor_gain | 1.0000 |
| 17:42582807:C:CC | acceptor_gain | 1.0000 |
| 17:42582808:T:C | acceptor_gain | 1.0000 |
| 17:42582808:T:TC | acceptor_gain | 1.0000 |
| 17:42582821:A:T | acceptor_gain | 1.0000 |
| 17:42583493:GATAC:G | donor_loss | 1.0000 |
| 17:42583494:ATACC:A | donor_loss | 1.0000 |
| 17:42583495:TACCT:T | donor_loss | 1.0000 |
| 17:42583496:A:AT | donor_loss | 1.0000 |
| 17:42583497:C:CG | donor_loss | 1.0000 |
| 17:42583499:TGAGG:T | donor_gain | 1.0000 |
| 17:42583576:GCGTA:G | acceptor_gain | 1.0000 |
| 17:42583577:CGTA:C | acceptor_gain | 1.0000 |
| 17:42583577:CGTAC:C | acceptor_gain | 1.0000 |
| 17:42583578:GTA:G | acceptor_gain | 1.0000 |
| 17:42583579:TA:T | acceptor_gain | 1.0000 |
| 17:42583580:ACTG:A | acceptor_loss | 1.0000 |
| 17:42583581:C:CC | acceptor_gain | 1.0000 |
| 17:42583581:C:G | acceptor_loss | 1.0000 |
AlphaMissense
3029 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 17:42586783:T:A | K162N | 0.997 |
| 17:42586783:T:G | K162N | 0.997 |
| 17:42586135:G:C | F169L | 0.996 |
| 17:42586135:G:T | F169L | 0.996 |
| 17:42586137:A:G | F169L | 0.996 |
| 17:42581873:A:C | F447L | 0.995 |
| 17:42581873:A:T | F447L | 0.995 |
| 17:42581875:A:G | F447L | 0.995 |
| 17:42581874:A:C | F447C | 0.994 |
| 17:42586123:G:C | S173R | 0.993 |
| 17:42586123:G:T | S173R | 0.993 |
| 17:42586125:T:G | S173R | 0.993 |
| 17:42582717:G:C | F300L | 0.990 |
| 17:42582717:G:T | F300L | 0.990 |
| 17:42582719:A:G | F300L | 0.990 |
| 17:42586784:T:A | K162I | 0.989 |
| 17:42592086:A:G | W106R | 0.989 |
| 17:42592086:A:T | W106R | 0.989 |
| 17:42583507:G:C | F267L | 0.988 |
| 17:42583507:G:T | F267L | 0.988 |
| 17:42583509:A:G | F267L | 0.988 |
| 17:42586122:A:G | C174R | 0.988 |
| 17:42609141:A:G | W62R | 0.988 |
| 17:42609141:A:T | W62R | 0.988 |
| 17:42586134:A:G | C170R | 0.987 |
| 17:42586136:A:G | F169S | 0.986 |
| 17:42592098:A:G | C102R | 0.986 |
| 17:42582236:A:C | F326L | 0.983 |
| 17:42582236:A:T | F326L | 0.983 |
| 17:42582238:A:G | F326L | 0.983 |
dbSNP variants (sampled 300 via entrez): RS1000082779 (17:42605009 G>A,C), RS1000205705 (17:42589285 A>C,G), RS1000266418 (17:42604683 C>T), RS1000371644 (17:42599687 G>T), RS1000543364 (17:42604368 T>C), RS1000627953 (17:42579617 C>A), RS1000637859 (17:42605711 G>A,C), RS1000691492 (17:42597696 TCTC>T), RS1000847302 (17:42591270 T>C), RS1000999074 (17:42604588 G>A), RS1000999620 (17:42584134 T>A), RS1001113921 (17:42583876 C>T), RS1001232470 (17:42579943 A>G), RS1001240843 (17:42607020 TA>T), RS1001246946 (17:42579036 G>A)
Disease associations
OMIM: gene MIM:616498 | disease phenotypes: MIM:615412
GenCC curated gene-disease
Mondo (1): complex cortical dysplasia with other brain malformations 4 (MONDO:0014171)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST009325_53 | Parkinson’s disease or first degree relation to individual with Parkinson’s disease | 1.000000e-09 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
34 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases expression | 3 |
| Arsenic | affects methylation, decreases expression, increases abundance | 2 |
| Cadmium Chloride | decreases expression, increases abundance, increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| testosterone enanthate | affects expression | 1 |
| bisphenol A | increases expression | 1 |
| trichostatin A | affects expression | 1 |
| sodium arsenite | decreases expression, increases abundance | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| ochratoxin A | decreases expression | 1 |
| potassium chromate(VI) | increases expression | 1 |
| coumarin | decreases phosphorylation | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| bisphenol S | increases expression | 1 |
| bisphenol AF | increases expression | 1 |
| Sunitinib | increases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Air Pollutants | increases abundance, decreases expression | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Caffeine | affects phosphorylation | 1 |
| Estradiol | decreases expression | 1 |
| Ethyl Methanesulfonate | increases expression | 1 |
| Formaldehyde | increases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Methyl Methanesulfonate | increases expression | 1 |
| Thiram | decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Urethane | increases expression | 1 |
| Vanadates | decreases expression | 1 |
Cellosaurus cell lines
15 cell lines: 15 embryonic stem cell
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_D1IA | H9 AAVS1-TRE3G-NGN2 RETREG3-/- | Embryonic stem cell | Female |
| CVCL_D1IB | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- | Embryonic stem cell | Female |
| CVCL_D1IC | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- | Embryonic stem cell | Female |
| CVCL_D1ID | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- TEX264-/- | Embryonic stem cell | Female |
| CVCL_D1IE | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- TEX264-/- CCPG1-/- | Embryonic stem cell | Female |
| CVCL_D1IP | H9 AAVS1-TRE3G-NGN2 RETREG3-/- Keima-RAMP4 | Embryonic stem cell | Female |
| CVCL_D1IQ | H9 AAVS1-TRE3G-NGN2 RETREG3-/- Keima-REEP5 | Embryonic stem cell | Female |
| CVCL_D1IR | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- Keima-RAMP4 | Embryonic stem cell | Female |
| CVCL_D1IS | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- Keima-REEP5 | Embryonic stem cell | Female |
| CVCL_D1IT | H9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- Keima-RAMP4 | Embryonic stem cell | Female |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): complex cortical dysplasia with other brain malformations 4