AAR2
gene geneOn this page
Also known as bA234K24.2
Summary
AAR2 (AAR2 splicing factor, HGNC:15886) is a protein-coding gene on chromosome 20q11.23, encoding Protein AAR2 homolog (Q9Y312). Component of the U5 snRNP complex that is required for spliceosome assembly and for pre-mRNA splicing.
This gene encodes the homolog of the yeast A1-alpha2 repressin protein that is involved in mRNA splicing. Alternately spliced transcript variants have been found for this gene.
Source: NCBI Gene 25980 — RefSeq curated summary.
At a glance
- Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Limited, GenCC)
- GWAS associations: 4
- Clinical variants (ClinVar): 73 total — 5 pathogenic, 2 likely-pathogenic
- Phenotypes (HPO): 3
- MANE Select transcript:
NM_001271874
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:15886 |
| Approved symbol | AAR2 |
| Name | AAR2 splicing factor |
| Location | 20q11.23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | bA234K24.2 |
| Ensembl gene | ENSG00000131043 |
| Ensembl biotype | protein_coding |
| OMIM | 617365 |
| Entrez | 25980 |
Gene structure
Transcript identifiers
Ensembl transcripts: 27 — 24 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay
ENST00000320849, ENST00000373932, ENST00000397286, ENST00000679519, ENST00000679667, ENST00000680185, ENST00000680247, ENST00000680412, ENST00000680639, ENST00000680811, ENST00000680933, ENST00000681771, ENST00000873086, ENST00000873087, ENST00000873088, ENST00000873089, ENST00000873090, ENST00000921595, ENST00000921596, ENST00000921597, ENST00000921598, ENST00000921599, ENST00000921600, ENST00000957173, ENST00000957174, ENST00000957175, ENST00000957176
RefSeq mRNA: 2 — MANE Select: NM_001271874
NM_001271874, NM_015511
CCDS: CCDS13273
Canonical transcript exons
ENST00000320849 — 4 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000661758 | 36244697 | 36244926 |
| ENSE00000860355 | 36239821 | 36240625 |
| ENSE00001413579 | 36236478 | 36236503 |
| ENSE00001902927 | 36255578 | 36256933 |
Expression profiles
Bgee: expression breadth ubiquitous, 262 present calls, max score 90.82.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8875 / max 57.5152, expressed in 1798 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 184385 | 13.9907 | 1793 |
| 184387 | 0.7348 | 469 |
| 184386 | 0.1620 | 41 |
Top tissues by expression
280 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| lower esophagus muscularis layer | UBERON:0035833 | 90.82 | gold quality |
| lower esophagus | UBERON:0013473 | 90.80 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 90.69 | gold quality |
| popliteal artery | UBERON:0002250 | 90.01 | gold quality |
| tibial artery | UBERON:0007610 | 90.00 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 89.89 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 89.42 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 89.26 | gold quality |
| aorta | UBERON:0000947 | 88.96 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 88.88 | gold quality |
| right coronary artery | UBERON:0001625 | 88.69 | gold quality |
| right adrenal gland | UBERON:0001233 | 88.62 | gold quality |
| pancreatic ductal cell | CL:0002079 | 88.60 | silver quality |
| islet of Langerhans | UBERON:0000006 | 88.51 | gold quality |
| type B pancreatic cell | CL:0000169 | 88.50 | gold quality |
| left coronary artery | UBERON:0001626 | 88.45 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 88.43 | gold quality |
| coronary artery | UBERON:0001621 | 88.16 | gold quality |
| left uterine tube | UBERON:0001303 | 88.07 | gold quality |
| olfactory bulb | UBERON:0002264 | 88.05 | gold quality |
| body of stomach | UBERON:0001161 | 88.01 | gold quality |
| left adrenal gland | UBERON:0001234 | 87.96 | gold quality |
| mucosa of stomach | UBERON:0001199 | 87.93 | gold quality |
| skin of leg | UBERON:0001511 | 87.90 | gold quality |
| thoracic aorta | UBERON:0001515 | 87.70 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 87.64 | gold quality |
| stromal cell of endometrium | CL:0002255 | 87.63 | gold quality |
| ascending aorta | UBERON:0001496 | 87.50 | gold quality |
| gastrocnemius | UBERON:0001388 | 87.48 | gold quality |
| adrenal cortex | UBERON:0001235 | 87.24 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 8.35 |
| E-MTAB-4850 | no | 953.26 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): NACC1, SPI1, TP53
miRNA regulators (miRDB)
51 targeting AAR2, 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-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-3185 | 99.99 | 68.12 | 1959 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-493-5P | 99.96 | 72.47 | 2382 |
| HSA-MIR-5682 | 99.89 | 72.56 | 1005 |
| HSA-MIR-4496 | 99.88 | 68.89 | 2236 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-182-5P | 99.87 | 74.03 | 2589 |
| HSA-MIR-6079 | 99.84 | 68.54 | 1170 |
| HSA-MIR-4306 | 99.72 | 70.50 | 3630 |
| HSA-MIR-6752-3P | 99.72 | 66.71 | 1587 |
| HSA-MIR-4261 | 99.59 | 70.30 | 3415 |
| HSA-MIR-6758-3P | 99.57 | 67.55 | 1078 |
| HSA-MIR-4276 | 99.56 | 67.66 | 2514 |
| HSA-MIR-1207-5P | 99.49 | 69.11 | 2983 |
| HSA-MIR-147B-5P | 99.45 | 70.62 | 2432 |
| HSA-MIR-2392 | 99.43 | 67.50 | 708 |
| HSA-MIR-5695 | 99.41 | 67.48 | 1047 |
| HSA-MIR-519D-5P | 99.41 | 69.30 | 2057 |
| HSA-MIR-185-5P | 99.35 | 68.60 | 2497 |
| HSA-MIR-4644 | 99.35 | 69.12 | 2514 |
| HSA-MIR-6828-5P | 99.31 | 69.21 | 1433 |
| HSA-MIR-10522-5P | 99.26 | 68.50 | 2087 |
| HSA-MIR-6768-3P | 99.14 | 67.38 | 1319 |
| HSA-MIR-3125 | 99.14 | 68.49 | 2269 |
| HSA-MIR-4763-3P | 99.10 | 67.83 | 2649 |
| HSA-MIR-1286 | 99.09 | 66.23 | 1046 |
| HSA-MIR-6830-5P | 99.01 | 68.73 | 1884 |
Literature-anchored findings (GeneRIF, showing 2)
- Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis. (PMID:36191209)
- Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8. (PMID:36322420)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | aar2 | ENSDARG00000018658 |
| mus_musculus | Aar2 | ENSMUSG00000027628 |
| rattus_norvegicus | Aar2 | ENSRNOG00000020086 |
| drosophila_melanogaster | CG12320 | FBGN0038590 |
| caenorhabditis_elegans | WBGENE00008639 |
Protein
Protein identifiers
Protein AAR2 homolog — Q9Y312 (reviewed: Q9Y312)
Alternative names: AAR2 splicing factor homolog
All UniProt accessions (4): Q9Y312, A0A7P0T8J7, A0A7P0TA70, A2A2Q9
UniProt curated annotations — full annotation on UniProt →
Function. Component of the U5 snRNP complex that is required for spliceosome assembly and for pre-mRNA splicing.
Subunit / interactions. Interacts with PRPF8 (via RNase H homology domain). Component of a U5 snRNP complex that contains PRPF8.
Similarity. Belongs to the AAR2 family.
RefSeq proteins (2): NP_001258803, NP_056326 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR007946 | AAR2 | Family |
| IPR033647 | Aar2_N | Domain |
| IPR033648 | AAR2_C | Domain |
| IPR038514 | AAR2_C_sf | Homologous_superfamily |
| IPR038516 | AAR2_N_sf | Homologous_superfamily |
Pfam: PF05282, PF20981
UniProt features (39 total): helix 16, strand 10, sequence conflict 8, initiator methionine 1, chain 1, modified residue 1, turn 1, sequence variant 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 7PJH | X-RAY DIFFRACTION | 2.35 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9Y312-F1 | 89.74 | 0.72 |
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 (1): 2
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 119 (showing top):
NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, CEBPB_01, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, TTGGAGA_MIR5155P_MIR519E, GOBP_REGULATION_OF_MRNA_SPLICING_VIA_SPLICEOSOME, GCM_NF2, chr20q11, MODULE_207, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, LIAN_LIPA_TARGETS_3M
GO Biological Process (3): spliceosomal tri-snRNP complex assembly (GO:0000244), mRNA processing (GO:0006397), RNA splicing (GO:0008380)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (2): spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| RNA processing | 2 |
| spliceosomal snRNP assembly | 1 |
| mRNA metabolic process | 1 |
| binding | 1 |
| nuclear protein-containing complex | 1 |
| ribonucleoprotein complex | 1 |
| spliceosomal snRNP complex | 1 |
Protein interactions and networks
STRING
2152 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| AAR2 | EFTUD2 | Q15029 | 916 |
| AAR2 | SNRNP200 | O75643 | 907 |
| AAR2 | PRPF8 | Q6P2Q9 | 814 |
| AAR2 | ZNHIT2 | Q9UHR6 | 748 |
| AAR2 | CD2BP2 | O95400 | 689 |
| AAR2 | ECD | O95905 | 672 |
| AAR2 | COPS5 | Q92905 | 647 |
| AAR2 | NCDN | Q9UBB6 | 611 |
| AAR2 | PRPF6 | O94906 | 605 |
| AAR2 | DDX23 | Q9BUQ8 | 593 |
| AAR2 | TXNL4A | P83876 | 569 |
| AAR2 | RUVBL2 | Q9Y230 | 564 |
| AAR2 | RUVBL1 | P82276 | 559 |
| AAR2 | PRPF31 | Q8WWY3 | 549 |
| AAR2 | PIH1D1 | Q9NWS0 | 539 |
| AAR2 | SNU13 | P55769 | 539 |
IntAct
77 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SNRPF | GEMIN2 | psi-mi:“MI:0914”(association) | 0.910 |
| SMARCC2 | ARID1A | psi-mi:“MI:0914”(association) | 0.790 |
| CFTR | ESYT2 | psi-mi:“MI:0914”(association) | 0.710 |
| SNRPD2 | GEMIN2 | psi-mi:“MI:0914”(association) | 0.710 |
| SNRPB | PRMT5 | psi-mi:“MI:0914”(association) | 0.670 |
| AAR2 | EAPP | psi-mi:“MI:0915”(physical association) | 0.660 |
| PMPCB | psi-mi:“MI:0914”(association) | 0.640 | |
| PRPF8 | PRPF4 | psi-mi:“MI:0914”(association) | 0.640 |
| DDX23 | PRPF4 | psi-mi:“MI:0914”(association) | 0.640 |
| EFTUD2 | SART1 | psi-mi:“MI:0914”(association) | 0.610 |
| AAR2 | SNRNP200 | psi-mi:“MI:0914”(association) | 0.530 |
| KIAA1143 | AQR | psi-mi:“MI:0914”(association) | 0.530 |
| EAPP | SNRNP200 | psi-mi:“MI:0914”(association) | 0.530 |
| EFTUD2 | AQR | psi-mi:“MI:0914”(association) | 0.530 |
| ECD | SNRNP200 | psi-mi:“MI:0914”(association) | 0.530 |
| KLHL36 | HSPA8 | psi-mi:“MI:0914”(association) | 0.530 |
| PTGES3 | AIP | psi-mi:“MI:0914”(association) | 0.530 |
| SNRPE | PRMT5 | psi-mi:“MI:0914”(association) | 0.530 |
| SNRPN | PRMT5 | psi-mi:“MI:0914”(association) | 0.530 |
| SNRNP40 | AQR | psi-mi:“MI:0914”(association) | 0.530 |
| DDX23 | SNRNP200 | psi-mi:“MI:0914”(association) | 0.530 |
| Cdk1 | psi-mi:“MI:0915”(physical association) | 0.400 |
BioGRID (777): AAR2 (Affinity Capture-MS), AAR2 (Affinity Capture-MS), AAR2 (Affinity Capture-MS), SNRNP200 (Affinity Capture-MS), PRPF8 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), TTC5 (Affinity Capture-MS), GHDC (Affinity Capture-MS), ECD (Affinity Capture-MS), NCDN (Affinity Capture-MS), SLC7A6OS (Affinity Capture-MS), MICA (Affinity Capture-MS), ZNHIT2 (Affinity Capture-MS), KLHL36 (Affinity Capture-MS), EAPP (Two-hybrid)
ESM2 similar proteins: A0AUR5, A0JNG7, A2VE39, A5PKL6, A8MYZ0, B0BM95, B0V3H4, B5DG51, D2HRF1, O02697, P48736, P60670, Q0IIH8, Q4KLT3, Q4R4D7, Q4R528, Q4R6Y8, Q4R760, Q4V8W7, Q5R981, Q5RBW9, Q5RL51, Q5U2Z5, Q5XH30, Q68EP9, Q6NX27, Q7ZYP6, Q803A6, Q803R5, Q80V94, Q811C2, Q8CD92, Q8CDM8, Q8K4M9, Q8N1G2, Q8NEC7, Q8R3N6, Q8TAT6, Q8VDY4, Q91WR3
Diamond homologs: O77682, Q08DJ7, Q09305, Q4R7D0, Q5R5N9, Q9D2V5, Q9Y312
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 86 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 |
|---|---|---|---|
| Metabolism of non-coding RNA | 6 | 64.5× | 2e-08 |
| mRNA Splicing - Minor Pathway | 11 | 41.8× | 2e-13 |
| snRNP Assembly | 7 | 25.1× | 6e-07 |
| SARS-CoV-2 modulates host translation machinery | 6 | 22.8× | 9e-06 |
| mRNA Splicing | 11 | 20.5× | 5e-10 |
| mRNA Splicing - Major Pathway | 19 | 17.6× | 1e-16 |
| Processing of Capped Intron-Containing Pre-mRNA | 11 | 15.3× | 8e-09 |
| The role of GTSE1 in G2/M progression after G2 checkpoint | 5 | 13.6× | 9e-04 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| spliceosomal snRNP assembly | 9 | 69.7× | 1e-12 |
| RNA splicing, via transesterification reactions | 6 | 49.9× | 2e-07 |
| U2-type prespliceosome assembly | 5 | 41.6× | 1e-05 |
| mRNA splicing, via spliceosome | 19 | 23.2× | 2e-18 |
| RNA splicing | 13 | 15.3× | 4e-10 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
73 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 5 |
| Likely pathogenic | 2 |
| Uncertain significance | 56 |
| Likely benign | 4 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (7)
| Variant ID | HGVS | Classification |
|---|---|---|
| 146117 | GRCh38/hg38 20q11.21-11.23(chr20:33432363-36821881)x1 | Pathogenic |
| 146596 | GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 | Pathogenic |
| 443340 | GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 | Pathogenic |
| 59195 | GRCh38/hg38 20p12.2-q12(chr20:9811433-39316956)x3 | Pathogenic |
| 689044 | GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3 | Pathogenic |
| 1809278 | GRCh37/hg19 20q11.21-11.23(chr20:29652122-35603726)x3 | Likely pathogenic |
| 242897 | NM_001271874.2(AAR2):c.520G>A (p.Val174Met) | Likely pathogenic |
SpliceAI
761 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 20:36239819:A:AG | acceptor_gain | 1.0000 |
| 20:36239819:A:T | acceptor_loss | 1.0000 |
| 20:36239819:AGCT:A | acceptor_gain | 1.0000 |
| 20:36239820:G:GA | acceptor_gain | 1.0000 |
| 20:36239820:GC:G | acceptor_gain | 1.0000 |
| 20:36239820:GCT:G | acceptor_gain | 1.0000 |
| 20:36239820:GCTG:G | acceptor_gain | 1.0000 |
| 20:36239820:GCTGT:G | acceptor_gain | 1.0000 |
| 20:36240616:G:GT | donor_gain | 1.0000 |
| 20:36244692:TTCA:T | acceptor_loss | 1.0000 |
| 20:36244694:CAG:C | acceptor_loss | 1.0000 |
| 20:36244695:AGGT:A | acceptor_gain | 1.0000 |
| 20:36244696:GGT:G | acceptor_gain | 1.0000 |
| 20:36244696:GGTG:G | acceptor_gain | 1.0000 |
| 20:36244925:AGG:A | donor_loss | 1.0000 |
| 20:36244926:GGTGA:G | donor_loss | 1.0000 |
| 20:36244928:T:G | donor_loss | 1.0000 |
| 20:36236500:GGCG:G | donor_gain | 0.9900 |
| 20:36236501:GCGG:G | donor_gain | 0.9900 |
| 20:36236783:G:GG | donor_gain | 0.9900 |
| 20:36239816:CTCAG:C | acceptor_gain | 0.9900 |
| 20:36239817:TCAG:T | acceptor_gain | 0.9900 |
| 20:36239818:CAGCT:C | acceptor_gain | 0.9900 |
| 20:36239819:AGCTG:A | acceptor_gain | 0.9900 |
| 20:36239822:T:A | acceptor_gain | 0.9900 |
| 20:36240621:GCTTG:G | donor_gain | 0.9900 |
| 20:36240622:CTTGG:C | donor_loss | 0.9900 |
| 20:36240623:TTGGT:T | donor_loss | 0.9900 |
| 20:36240624:TGGT:T | donor_loss | 0.9900 |
| 20:36240626:G:A | donor_loss | 0.9900 |
AlphaMissense
2542 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 20:36240265:T:A | W133R | 0.999 |
| 20:36240265:T:C | W133R | 0.999 |
| 20:36240001:T:C | F45L | 0.998 |
| 20:36240003:C:A | F45L | 0.998 |
| 20:36240003:C:G | F45L | 0.998 |
| 20:36240034:C:G | H56D | 0.998 |
| 20:36244759:T:A | W274R | 0.998 |
| 20:36244759:T:C | W274R | 0.998 |
| 20:36255654:T:C | L355P | 0.998 |
| 20:36240241:T:G | Y125D | 0.997 |
| 20:36244703:T:C | L255P | 0.997 |
| 20:36255671:T:A | W361R | 0.997 |
| 20:36255671:T:C | W361R | 0.997 |
| 20:36240007:G:C | G47R | 0.996 |
| 20:36240008:G:A | G47D | 0.996 |
| 20:36240015:G:C | K49N | 0.996 |
| 20:36240015:G:T | K49N | 0.996 |
| 20:36244714:T:C | F259L | 0.996 |
| 20:36244716:T:A | F259L | 0.996 |
| 20:36244716:T:G | F259L | 0.996 |
| 20:36244720:T:C | C261R | 0.996 |
| 20:36244761:G:C | W274C | 0.996 |
| 20:36244761:G:T | W274C | 0.996 |
| 20:36244905:C:A | N322K | 0.996 |
| 20:36244905:C:G | N322K | 0.996 |
| 20:36244910:T:A | L324H | 0.996 |
| 20:36239971:G:C | D35H | 0.995 |
| 20:36240002:T:C | F45S | 0.995 |
| 20:36240094:G:C | G76R | 0.995 |
| 20:36240267:G:C | W133C | 0.995 |
dbSNP variants (sampled 300 via entrez): RS1000014282 (20:36256446 C>T), RS1000142299 (20:36237378 G>A,C), RS1000231495 (20:36253374 A>G), RS1000680916 (20:36244509 G>A), RS1000962831 (20:36246282 C>T), RS1001065492 (20:36247518 CTT>C), RS1001115790 (20:36244783 T>G), RS1001340116 (20:36240749 T>C), RS1001472021 (20:36252405 C>G,T), RS1001574383 (20:36238406 C>G), RS1001610059 (20:36243597 T>A), RS1001818010 (20:36252646 C>T), RS1002096307 (20:36237044 A>G), RS1002180324 (20:36240113 A>C,T), RS1002279726 (20:36247122 T>C)
Disease associations
OMIM: gene MIM:617365 | disease phenotypes: MIM:614429
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| multiple congenital anomalies/dysmorphic syndrome | Limited | Autosomal recessive |
Mondo (4): microcephaly (MONDO:0001149), ventricular septal defect (MONDO:0002070), patent foramen ovale (MONDO:0020439), multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)
Orphanet (3): Cerebellar malformation (Orphanet:182061), NON RARE IN EUROPE: Ventricular septal defect (Orphanet:1480), NON RARE IN EUROPE: Patent foramen ovale (Orphanet:99108)
HPO phenotypes
3 total (3 of 3 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000252 | Microcephaly |
| HP:0001629 | Ventricular septal defect |
| HP:0001655 | Patent foramen ovale |
GWAS associations
4 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST001762_220 | Obesity-related traits | 4.000000e-06 |
| GCST010002_66 | Refractive error | 2.000000e-20 |
| GCST012227_1105 | Hip circumference adjusted for BMI | 2.000000e-11 |
| GCST90020029_197 | Waist circumference adjusted for body mass index | 3.000000e-08 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0003940 | physical activity |
| EFO:0008039 | BMI-adjusted hip circumference |
| EFO:0007789 | BMI-adjusted waist circumference |
MeSH disease descriptors (3)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D054092 | Foramen Ovale, Patent | C14.240.400.560.375.258; C14.280.400.560.375.258; C16.131.240.400.560.375.258 |
| D006345 | Heart Septal Defects, Ventricular | C14.240.400.560.540; C14.280.400.560.540; C16.131.240.400.560.540 |
| D008831 | Microcephaly | C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
23 total (human), top 23 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | increases expression, increases methylation | 3 |
| bisphenol A | affects cotreatment, increases methylation, increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| 2,4,6-tribromophenol | decreases expression | 1 |
| decabromobiphenyl ether | decreases expression | 1 |
| cobaltous chloride | increases expression | 1 |
| potassium chromate(VI) | affects cotreatment, increases expression | 1 |
| epigallocatechin gallate | affects cotreatment, increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | decreases expression | 1 |
| pentabrominated diphenyl ether 100 | increases expression | 1 |
| bisphenol S | increases expression | 1 |
| Fulvestrant | affects cotreatment, increases methylation | 1 |
| Leflunomide | decreases expression | 1 |
| Arsenic | increases methylation | 1 |
| Benzene | increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Phthalic Acids | decreases methylation | 1 |
| Smoke | decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Tretinoin | decreases expression | 1 |
| Cadmium Chloride | decreases expression | 1 |
Cellosaurus cell lines
2 cell lines: 2 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_E1IC | HAP1 AAR2 (-) 1 | Cancer cell line | Male |
| CVCL_E1ID | HAP1 AAR2 (-) 2 | Cancer cell line | Male |
Clinical trials (associated diseases)
145 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT02914652 | PHASE4 | COMPLETED | The Cardiopulmonary Effect of Inhaled Beta-2-agonists on Adult Patients Born With Ventricular Septum Defects. |
| NCT05688670 | PHASE4 | COMPLETED | Regional Anesthesia Following Pediatric Cardiac Surgery |
| NCT00697151 | PHASE4 | COMPLETED | Patent Foramen Ovale in Cryptogenic Stroke Study |
| NCT01550588 | PHASE4 | UNKNOWN | Device Closure Versus Medical Therapy for Cryptogenic Stroke Patients With High-Risk Patent Foramen Ovale (DEFENSE-PFO) |
| NCT05561660 | PHASE4 | UNKNOWN | COMParison of the EffecT of dEvice Closure in Alleviating Migraine With PFO (COMPETE-2) |
| NCT00000470 | PHASE3 | COMPLETED | Infant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest |
| NCT00113698 | PHASE3 | TERMINATED | Angiotensin Converting Enzyme Inhibition in Children With Mitral Regurgitation |
| NCT05253209 | PHASE3 | TERMINATED | A Study Evaluating the Efficacy and Safety of IV L-Citrulline for the Prevention of Clinical Sequelae of Acute Lung Injury Induced by Cardiopulmonary Bypass in Pediatric Patients Undergoing Surgery for Congenital Heart Defects |
| NCT00562289 | PHASE3 | COMPLETED | Patent Foramen Ovale Closure or Anticoagulants Versus Antiplatelet Therapy to Prevent Stroke Recurrence |
| NCT01333761 | PHASE3 | TERMINATED | Cardiox Shunt Detection Technology Study |
| NCT01773252 | PHASE3 | TERMINATED | Right to Left Cardiac Shunt Detection |
| NCT05213104 | PHASE3 | ACTIVE_NOT_RECRUITING | Assessment of Flecainide to Lower the Patent Foramen Ovale Closure Risk of Atrial Arrhythmia or Tachycardia |
| NCT05387954 | PHASE3 | RECRUITING | PFO Closure, Oral Anticoagulants or Antiplatelet Therapy After PFO-associated Stroke in Patients Aged 60 to 80 Years |
| NCT00199771 | PHASE2 | COMPLETED | Hypertonic Saline Dextran in Pediatric Cardiac Surgery |
| NCT00556361 | PHASE2 | COMPLETED | Use of Ketamine Prior to Cardiopulmonary Bypass in Children |
| NCT00848393 | PHASE2 | COMPLETED | Measures to Lower the Stress Response in Pediatric Cardiac Surgery |
| NCT04017975 | PHASE2 | ACTIVE_NOT_RECRUITING | Optical Tissue Identification for Myocardial Architecture |
| NCT00505570 | PHASE2 | TERMINATED | PRIMA PFO Migraine Trial |
| NCT02378623 | PHASE2 | WITHDRAWN | Patients With Patent Foramen Ovale and Endocardial Device Leads on Apixaban for Prevention of Paradoxical Emboli |
| NCT02777359 | PHASE2 | UNKNOWN | Precutaneous High Risk Patent Foramen Ovale to Treat Migraine Headaches |
| NCT05546320 | PHASE2 | COMPLETED | Comparison of the Effect of Medication Therapy in Alleviating Migraine With Patent Foramen Ovale |
| NCT01825369 | PHASE1 | WITHDRAWN | Aberrations in Carnitine Homeostasis in Congenital Heart Disease With Increased Pulmonary Blood Flow |
| NCT01915277 | PHASE1 | COMPLETED | A Phase I Study of Dexmedetomidine Bolus and Infusion in Corrective Infant Cardiac Surgery: Safety and Pharmacokinetics |
| NCT05518188 | PHASE1/PHASE2 | RECRUITING | Melpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt) |
| NCT00001639 | Not specified | COMPLETED | Evaluation of Patients With Unresolved Chromosome Abnormalities |
| NCT01151462 | Not specified | WITHDRAWN | Postnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes. |
| NCT01565005 | Not specified | COMPLETED | Microcephaly Genetic Deficiency in Neural Progenitors |
| NCT02510170 | Not specified | COMPLETED | Fetal and Maternal Head Circumference During Pregnancy in Israeli Population |
| NCT02741882 | Not specified | COMPLETED | Zika and Microcephaly: Case-control Study |
| NCT02943304 | Not specified | COMPLETED | Neurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero |
| NCT03255369 | Not specified | UNKNOWN | Vertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF) |
| NCT03325946 | Not specified | RECRUITING | The FBRI VTC Neuromotor Research Clinic |
| NCT03330600 | Not specified | COMPLETED | Efficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome |
| NCT03548779 | Not specified | COMPLETED | North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2 |
| NCT03651687 | Not specified | COMPLETED | Guangzhou Surveillance and Clinical Study in Microcephaly (GSCSM) |
| NCT03922594 | Not specified | TERMINATED | Surveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia |
| NCT04816175 | Not specified | COMPLETED | Intensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay |
| NCT05322980 | Not specified | COMPLETED | Summary of Infants Weighing 500 Grams or Less |
| NCT06019182 | Not specified | RECRUITING | MEHMO Natural History and Biomarkers |
| NCT06566066 | Not specified | RECRUITING | Register for Patients With Thyroid Hormone Resistance. |
Related Atlas pages
- Associated diseases: multiple congenital anomalies/dysmorphic syndrome
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): multiple congenital anomalies/dysmorphic syndrome, patent foramen ovale, ventricular septal defect