ZNF219
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Summary
ZNF219 (zinc finger protein 219, HGNC:13011) is a protein-coding gene on chromosome 14q11.2, encoding Zinc finger protein 219 (Q9P2Y4). Transcriptional regulator.
This gene is a member of the Kruppel-like zinc finger gene family. The encoded protein functions as a transcriptional repressor of the high mobility group nucleosome binding domain 1 protein, which is associated with transcriptionally active chromatin.
Source: NCBI Gene 51222 — RefSeq curated summary.
At a glance
- Gene–disease (curated): microphthalmia (Limited, GenCC)
- GWAS associations: 2
- Clinical variants (ClinVar): 96 total
- MANE Select transcript:
NM_016423
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:13011 |
| Approved symbol | ZNF219 |
| Name | zinc finger protein 219 |
| Location | 14q11.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000165804 |
| Ensembl biotype | protein_coding |
| OMIM | 605036 |
| Entrez | 51222 |
Gene structure
Transcript identifiers
Ensembl transcripts: 34 — 31 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 TEC
ENST00000360947, ENST00000421093, ENST00000451119, ENST00000553296, ENST00000553980, ENST00000554478, ENST00000554923, ENST00000555270, ENST00000555697, ENST00000556101, ENST00000556174, ENST00000556944, ENST00000624093, ENST00000878251, ENST00000878252, ENST00000878253, ENST00000878254, ENST00000878255, ENST00000878256, ENST00000878257, ENST00000878258, ENST00000918830, ENST00000918831, ENST00000918832, ENST00000918833, ENST00000918834, ENST00000918835, ENST00000918836, ENST00000918837, ENST00000918838, ENST00000918839, ENST00000918840, ENST00000950347, ENST00000950348
RefSeq mRNA: 3 — MANE Select: NM_016423
NM_001101672, NM_001102454, NM_016423
CCDS: CCDS9568
Canonical transcript exons
ENST00000360947 — 5 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001096720 | 21090077 | 21091140 |
| ENSE00001096722 | 21091865 | 21093290 |
| ENSE00001096724 | 21098312 | 21098655 |
| ENSE00001096726 | 21091411 | 21091542 |
| ENSE00003464740 | 21093586 | 21093674 |
Expression profiles
Bgee: expression breadth ubiquitous, 217 present calls, max score 96.74.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.3567 / max 206.9743, expressed in 1723 samples.
FANTOM5 promoters (9 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 142121 | 14.3985 | 1693 |
| 142120 | 1.1932 | 518 |
| 142122 | 0.6903 | 444 |
| 142119 | 0.3756 | 153 |
| 142117 | 0.2530 | 60 |
| 142123 | 0.1465 | 44 |
| 142116 | 0.1444 | 55 |
| 142125 | 0.0966 | 42 |
| 142118 | 0.0586 | 28 |
Top tissues by expression
254 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right adrenal gland | UBERON:0001233 | 96.74 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 96.61 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 96.58 | gold quality |
| left adrenal gland | UBERON:0001234 | 96.43 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 96.33 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 95.91 | gold quality |
| adrenal cortex | UBERON:0001235 | 95.67 | gold quality |
| lower esophagus | UBERON:0013473 | 95.57 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 95.55 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 95.47 | gold quality |
| apex of heart | UBERON:0002098 | 95.32 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 95.24 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 94.74 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 94.71 | gold quality |
| cerebellar cortex | UBERON:0002129 | 94.57 | gold quality |
| transverse colon | UBERON:0001157 | 94.52 | gold quality |
| esophagus | UBERON:0001043 | 93.86 | gold quality |
| adrenal gland | UBERON:0002369 | 93.67 | gold quality |
| skin of leg | UBERON:0001511 | 93.44 | gold quality |
| cerebellum | UBERON:0002037 | 93.22 | gold quality |
| mucosa of stomach | UBERON:0001199 | 93.21 | gold quality |
| esophagus mucosa | UBERON:0002469 | 93.21 | gold quality |
| skin of abdomen | UBERON:0001416 | 92.98 | gold quality |
| ectocervix | UBERON:0012249 | 92.75 | gold quality |
| right coronary artery | UBERON:0001625 | 92.55 | gold quality |
| ventricular zone | UBERON:0003053 | 92.55 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 92.48 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 92.43 | gold quality |
| ganglionic eminence | UBERON:0004023 | 92.36 | gold quality |
| right atrium auricular region | UBERON:0006631 | 92.30 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 4.82 |
Regulation
Is transcription factor: yes
Downstream targets (CollecTRI)
5 targets.
| Target | Regulation |
|---|---|
| ACAN | Activation |
| COL11A2 | Activation |
| COL2A1 | Activation |
| HMGN1 | |
| SNCA |
miRNA regulators (miRDB)
46 targeting ZNF219, 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-4283 | 100.00 | 66.42 | 2097 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-LET-7C-3P | 99.95 | 73.42 | 2862 |
| HSA-MIR-185-3P | 99.95 | 67.01 | 1743 |
| HSA-MIR-124-3P | 99.89 | 73.74 | 3043 |
| HSA-MIR-506-3P | 99.89 | 73.55 | 3057 |
| HSA-MIR-4492 | 99.87 | 68.25 | 3611 |
| HSA-MIR-6857-5P | 99.87 | 65.32 | 985 |
| HSA-MIR-6756-5P | 99.82 | 67.97 | 2466 |
| HSA-MIR-3150A-3P | 99.76 | 64.44 | 1640 |
| HSA-MIR-6763-5P | 99.76 | 64.68 | 1767 |
| HSA-MIR-6745 | 99.74 | 65.33 | 1321 |
| HSA-MIR-3714 | 99.71 | 70.74 | 2671 |
| HSA-MIR-6766-5P | 99.68 | 67.70 | 2325 |
| HSA-MIR-762 | 99.58 | 66.61 | 1994 |
| HSA-MIR-4489 | 99.50 | 65.56 | 785 |
| HSA-MIR-4498 | 99.47 | 67.42 | 2360 |
| HSA-MIR-5580-5P | 99.38 | 66.96 | 1139 |
| HSA-MIR-4505 | 99.27 | 67.81 | 2678 |
| HSA-MIR-5787 | 99.22 | 67.86 | 2628 |
| HSA-MIR-6780B-3P | 99.13 | 67.18 | 622 |
| HSA-MIR-6815-3P | 99.13 | 68.98 | 1530 |
| HSA-MIR-6868-5P | 99.06 | 65.69 | 1284 |
| HSA-MIR-5001-5P | 99.05 | 66.76 | 1972 |
| HSA-MIR-3154 | 98.94 | 66.55 | 1455 |
| HSA-MIR-6829-5P | 98.86 | 65.12 | 1480 |
| HSA-MIR-4656 | 98.79 | 66.22 | 1306 |
| HSA-MIR-210-5P | 98.57 | 64.37 | 832 |
| HSA-MIR-6810-5P | 98.29 | 66.21 | 975 |
| HSA-MIR-211-3P | 98.14 | 66.77 | 1052 |
Literature-anchored findings (GeneRIF, showing 4)
- By using a random oligonucleotide selection assay and the electromobility gel shift assay, we have revealed that the ZNF219 protein recognizes two copies of CCCCCA. (PMID:14621294)
- regulates chondrocyte differentiation as a transcriptional partner of Sox9 (PMID:20940257)
- ZNF219 protects human lens epithelial cells against H2O2-induced injury via targeting SOX9 through activating AKT/GSK3beta pathway. (PMID:34167360)
- ZNF219, a novel transcriptional repressor, inhibits transcription of the prototype foamy virus by interacting with the viral LTR promoter. (PMID:37356580)
Cross-species orthologs
8 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | znf516 | ENSDARG00000070809 |
| mus_musculus | Zfp219 | ENSMUSG00000049295 |
| rattus_norvegicus | Zfp219 | ENSRNOG00000011544 |
| drosophila_melanogaster | salr | FBGN0000287 |
| drosophila_melanogaster | Cph | FBGN0029939 |
| drosophila_melanogaster | salm | FBGN0261648 |
| caenorhabditis_elegans | sem-4 | WBGENE00004773 |
| caenorhabditis_elegans | WBGENE00017430 |
Paralogs (14): HIVEP2 (ENSG00000010818), HIVEP1 (ENSG00000095951), SALL4 (ENSG00000101115), ZNF516 (ENSG00000101493), SALL1 (ENSG00000103449), BCL11A (ENSG00000119866), ZNF831 (ENSG00000124203), RREB1 (ENSG00000124782), HIVEP3 (ENSG00000127124), BCL11B (ENSG00000127152), SALL2 (ENSG00000165821), ZNF217 (ENSG00000171940), ZNF536 (ENSG00000198597), SALL3 (ENSG00000256463)
Protein
Protein identifiers
Zinc finger protein 219 — Q9P2Y4 (reviewed: Q9P2Y4)
All UniProt accessions (8): Q9P2Y4, G3V2E3, G3V2Q8, G3V2W3, G3V3F2, G3V452, G3V4M7, G3V4T1
UniProt curated annotations — full annotation on UniProt →
Function. Transcriptional regulator. Recognizes and binds 2 copies of the core DNA sequence motif 5’-GGGGG-3’. Binds to the HMGN1 promoter and may repress HMGN1 expression. Regulates SNCA expression in primary cortical neurons. Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with SOX9. Plays a role in chondrocyte differentiation.
Subunit / interactions. Interacts with SOX9 (via C-terminus).
Subcellular location. Nucleus.
Tissue specificity. Ubiquitous.
Domain organisation. C2H2-type zinc-finger domains 5 and 6 are important for the interaction with SOX9.
Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.
RefSeq proteins (3): NP_001095142, NP_001095924, NP_057507* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR003980 | Histamine_H3_rcpt | Family |
| IPR013087 | Znf_C2H2_type | Domain |
| IPR036236 | Znf_C2H2_sf | Homologous_superfamily |
| IPR051967 | Krueppel_C2H2-ZF | Family |
Pfam: PF00096
UniProt features (31 total): zinc finger region 9, compositionally biased region 8, region of interest 6, modified residue 4, sequence conflict 2, chain 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9P2Y4-F1 | 56.46 | 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 (4): 16, 692, 695, 698
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 144 (showing top):
GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CARTILAGE_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, GTGCCTT_MIR506, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, GATA6_01, GOBP_CHONDROCYTE_DIFFERENTIATION, GOBP_APPENDAGE_DEVELOPMENT, GOBP_REGULATION_OF_CHONDROCYTE_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_CARTILAGE_DEVELOPMENT, AACTTT_UNKNOWN, KIM_GASTRIC_CANCER_CHEMOSENSITIVITY, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT
GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), positive regulation of chondrocyte differentiation (GO:0032332), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription by RNA polymerase II (GO:0045944), limb bud formation (GO:0060174), G protein-coupled receptor signaling pathway (GO:0007186)
GO Molecular Function (9): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), histamine receptor activity (GO:0004969), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)
GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| regulation of transcription by RNA polymerase II | 3 |
| RNA polymerase II transcription regulatory region sequence-specific DNA binding | 3 |
| transcription by RNA polymerase II | 2 |
| DNA-templated transcription | 2 |
| regulation of DNA-templated transcription | 2 |
| cellular anatomical structure | 2 |
| negative regulation of DNA-templated transcription | 1 |
| regulation of gene expression | 1 |
| regulation of RNA biosynthetic process | 1 |
| chondrocyte differentiation | 1 |
| regulation of chondrocyte differentiation | 1 |
| positive regulation of cell differentiation | 1 |
| positive regulation of cartilage development | 1 |
| negative regulation of RNA biosynthetic process | 1 |
| positive regulation of DNA-templated transcription | 1 |
| limb morphogenesis | 1 |
| anatomical structure formation involved in morphogenesis | 1 |
| G protein-coupled receptor activity | 1 |
| signal transduction | 1 |
| cis-regulatory region sequence-specific DNA binding | 1 |
| chromatin | 1 |
| DNA-binding transcription factor activity | 1 |
| negative regulation of transcription by RNA polymerase II | 1 |
| DNA-binding transcription factor activity, RNA polymerase II-specific | 1 |
| DNA-binding transcription repressor activity | 1 |
| nucleic acid binding | 1 |
| transcription cis-regulatory region binding | 1 |
| transcription regulator activity | 1 |
| G protein-coupled amine receptor activity | 1 |
| histamine binding | 1 |
| transition metal ion binding | 1 |
| binding | 1 |
| cation binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
Protein interactions and networks
STRING
962 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ZNF219 | HMGN1 | P05114 | 907 |
| ZNF219 | HMGN5 | P82970 | 750 |
| ZNF219 | HMGN2 | P05204 | 639 |
| ZNF219 | SOX9 | P48436 | 483 |
| ZNF219 | RNF141 | Q8WVD5 | 434 |
| ZNF219 | KRT24 | Q2M2I5 | 430 |
| ZNF219 | ETS2 | P15036 | 393 |
| ZNF219 | CTBP2 | P56545 | 388 |
| ZNF219 | WRAP53 | Q9BUR4 | 385 |
| ZNF219 | HOXB9 | P17482 | 383 |
| ZNF219 | DR1 | Q01658 | 383 |
| ZNF219 | ARID5A | Q03989 | 379 |
| ZNF219 | PIK3R5 | Q8WYR1 | 375 |
| ZNF219 | ZIC2 | O95409 | 373 |
| ZNF219 | SOX5 | P35711 | 358 |
IntAct
62 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| RBBP7 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.840 |
| HDAC1 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.840 |
| RBBP4 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.790 |
| HDAC1 | ZNF609 | psi-mi:“MI:0914”(association) | 0.730 |
| RBBP7 | HAT1 | psi-mi:“MI:0914”(association) | 0.730 |
| ZNF219 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.640 |
| LMO1 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TTC32 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ZNF219 | LMO1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ATOSB | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TRIM41 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UBASH3A | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| AP1M1 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| GRIPAP1 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ZNF219 | DR1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| KLHL40 | CBX4 | psi-mi:“MI:0914”(association) | 0.530 |
| MBD3L1 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF219 | RCCD1 | psi-mi:“MI:0914”(association) | 0.530 |
| NOTCH2 | ZNF316 | psi-mi:“MI:0914”(association) | 0.530 |
| CDK4 | ZNF219 | psi-mi:“MI:0217”(phosphorylation reaction) | 0.440 |
| ZNF219 | CSNK2A2 | psi-mi:“MI:0915”(physical association) | 0.370 |
| BCL2L1 | ZNF219 | psi-mi:“MI:0915”(physical association) | 0.370 |
BioGRID (147): ZNF219 (Two-hybrid), TTC32 (Two-hybrid), ZNF219 (Affinity Capture-MS), NPAT (Affinity Capture-MS), RBBP4 (Affinity Capture-MS), RBBP7 (Affinity Capture-MS), HDAC1 (Affinity Capture-MS), HDAC2 (Affinity Capture-MS), GATAD2B (Affinity Capture-MS), GATAD2A (Affinity Capture-MS), ZNF521 (Affinity Capture-MS), ZNF423 (Affinity Capture-MS), SPECC1L (Affinity Capture-MS), MBD2 (Affinity Capture-MS), MBD3 (Affinity Capture-MS)
ESM2 similar proteins: A2CE44, A6NFI3, A6NM28, A8K8V0, O15370, O70218, O95201, P0CJ78, P10075, P10754, P28698, P70338, Q04890, Q07120, Q14V87, Q19A40, Q569E7, Q58DK7, Q5DWN0, Q5FWU5, Q5RJR4, Q5T619, Q5TEC3, Q6DD87, Q6IQX8, Q6PD29, Q6PGE4, Q6ZMY9, Q7Z7K2, Q80VM4, Q8BIF9, Q8JZL0, Q8N8E2, Q8NAF0, Q8NCA9, Q8TD94, Q8WUU4, Q96C55, Q96H86, Q96MX3
Diamond homologs: A1L2U9, A2A884, A2ANX9, A7Y7X5, B0X9H6, B0YDH7, B1WAZ8, B1WBU4, E9PW05, E9PZZ1, G5EBU4, O15391, O60315, O62836, O75362, O77459, O95863, P08048, P0CS62, P0CS63, P10925, P15822, P17010, P17012, P20662, P22227, P25490, P28166, P31509, P31629, P36197, P52739, P52746, P56270, P56670, P56671, P60319, P80944, Q00899, Q00900
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 44 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.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Regulation of PTEN gene transcription | 6 | 33.5× | 4e-06 |
| NuRD complex assembly | 7 | 30.8× | 8e-07 |
| Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) | 6 | 27.4× | 8e-06 |
| Interaction of NuRD complexes with transcription factors | 5 | 19.8× | 3e-04 |
| Negative Regulation of CDH1 Gene Transcription | 5 | 18.8× | 3e-04 |
| Potential therapeutics for SARS | 5 | 17.8× | 4e-04 |
| Oxidative Stress Induced Senescence | 6 | 17.0× | 1e-04 |
| Regulation of endogenous retroelements by KRAB-ZFP proteins | 5 | 16.7× | 4e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
96 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 86 |
| Likely benign | 3 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2052 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 14:21091538:CTCTT:C | acceptor_gain | 1.0000 |
| 14:21091540:CTT:C | acceptor_gain | 1.0000 |
| 14:21091543:C:CC | acceptor_gain | 1.0000 |
| 14:21092005:T:TA | donor_gain | 1.0000 |
| 14:21101976:G:GG | donor_gain | 1.0000 |
| 14:21102777:G:GT | donor_gain | 1.0000 |
| 14:21091136:CTCGC:C | acceptor_gain | 0.9900 |
| 14:21091138:CGC:C | acceptor_gain | 0.9900 |
| 14:21091140:CCT:C | acceptor_loss | 0.9900 |
| 14:21091141:C:CC | acceptor_gain | 0.9900 |
| 14:21091142:T:A | acceptor_loss | 0.9900 |
| 14:21091405:CCTCA:C | donor_loss | 0.9900 |
| 14:21091407:TCACC:T | donor_loss | 0.9900 |
| 14:21091408:CAC:C | donor_loss | 0.9900 |
| 14:21091409:A:C | donor_loss | 0.9900 |
| 14:21091410:C:CT | donor_loss | 0.9900 |
| 14:21091541:TT:T | acceptor_gain | 0.9900 |
| 14:21091541:TTCTG:T | acceptor_loss | 0.9900 |
| 14:21091542:TCTGC:T | acceptor_loss | 0.9900 |
| 14:21091543:C:T | acceptor_loss | 0.9900 |
| 14:21091544:T:C | acceptor_loss | 0.9900 |
| 14:21091549:C:CT | acceptor_gain | 0.9900 |
| 14:21091552:A:C | acceptor_gain | 0.9900 |
| 14:21091863:AC:A | donor_gain | 0.9900 |
| 14:21091864:CC:C | donor_gain | 0.9900 |
| 14:21091987:T:TA | donor_gain | 0.9900 |
| 14:21092014:T:TA | donor_gain | 0.9900 |
| 14:21098310:A:AC | donor_gain | 0.9900 |
| 14:21098310:ACGAG:A | donor_gain | 0.9900 |
| 14:21098311:C:CC | donor_gain | 0.9900 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000157852 (14:21099224 A>G), RS1000195848 (14:21101178 A>C), RS1000510519 (14:21098894 C>T), RS1000534266 (14:21096153 C>A), RS1000630471 (14:21097343 C>CATGGGGGGG), RS1000708801 (14:21103235 C>T), RS1000739889 (14:21102860 G>A,T), RS1000952666 (14:21093835 A>C), RS1001006640 (14:21097995 A>C), RS1001110199 (14:21100789 C>T), RS1001941964 (14:21090110 C>A,T), RS1001973210 (14:21089793 G>A), RS1002262001 (14:21103636 T>C,G), RS1002606936 (14:21096096 C>G,T), RS1003104393 (14:21098016 C>A,G,T)
Disease associations
OMIM: gene MIM:605036 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| microphthalmia | Limited | Autosomal recessive |
Mondo (1): microphthalmia (MONDO:0021129)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003818_18 | Resting heart rate | 4.000000e-20 |
| GCST009391_203 | Metabolite levels | 7.000000e-06 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0010488 | glycerol-3-phosphate measurement |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D008850 | Microphthalmos | C11.250.566; C16.131.384.666 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
45 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, decreases expression, affects expression, increases methylation | 8 |
| trichostatin A | affects cotreatment, decreases expression | 3 |
| bisphenol A | decreases expression, decreases methylation, increases methylation | 2 |
| Air Pollutants | decreases expression, affects cotreatment, increases abundance, increases oxidation | 2 |
| Estradiol | affects cotreatment, decreases expression | 2 |
| Aflatoxin B1 | decreases methylation, increases expression | 2 |
| FR900359 | increases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| alpha-pinene | affects cotreatment, increases oxidation, increases abundance | 1 |
| beta-lapachone | decreases expression | 1 |
| arsenite | increases methylation | 1 |
| 1,6-hexamethylene diisocyanate | increases methylation | 1 |
| sodium arsenite | decreases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| methacrylaldehyde | affects cotreatment, increases oxidation, increases abundance | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | decreases expression, affects cotreatment | 1 |
| clothianidin | decreases expression | 1 |
| ICG 001 | increases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| bisphenol S | decreases methylation | 1 |
| MT19c compound | decreases expression | 1 |
| Vorinostat | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Acrolein | affects cotreatment, increases oxidation, increases abundance | 1 |
| Atrazine | increases expression | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Caffeine | decreases phosphorylation | 1 |
| Dichlorodiphenyl Dichloroethylene | decreases expression | 1 |
| Doxorubicin | decreases expression | 1 |
Clinical trials (associated diseases)
5 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT01778543 | Not specified | RECRUITING | Pathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC) |
| NCT03748732 | Not specified | UNKNOWN | Extensive Circumferential Partial Thickness Sclerectomy in Nanophthalmic Eyes |
| NCT04759560 | Not specified | UNKNOWN | Biometric Characteristics of the Eye With Microcornea/Microphthalmia and Congenital Cataract Before And After Cataract Extraction |
| NCT05954403 | Not specified | RECRUITING | National Cohort on Congenital Defects of the Eye |
| NCT06293560 | Not specified | RECRUITING | Microphthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children |
Related Atlas pages
- Associated diseases: microphthalmia
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): microphthalmia