PHLDA3
gene geneOn this page
Also known as TIH1
Summary
PHLDA3 (pleckstrin homology like domain family A member 3, HGNC:8934) is a protein-coding gene on chromosome 1q32.1, encoding Pleckstrin homology-like domain family A member 3 (Q9Y5J5). p53/TP53-regulated repressor of Akt/AKT1 signaling.
Enables phosphatidylinositol phosphate binding activity and phosphatidylinositol-3,4-bisphosphate binding activity. Involved in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator; negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction; and positive regulation of apoptotic process. Located in plasma membrane.
Source: NCBI Gene 23612 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 15 total
- MANE Select transcript:
NM_012396
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:8934 |
| Approved symbol | PHLDA3 |
| Name | pleckstrin homology like domain family A member 3 |
| Location | 1q32.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | TIH1 |
| Ensembl gene | ENSG00000174307 |
| Ensembl biotype | protein_coding |
| OMIM | 607054 |
| Entrez | 23612 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined
ENST00000367309, ENST00000367311, ENST00000485436, ENST00000497057
RefSeq mRNA: 1 — MANE Select: NM_012396
NM_012396
CCDS: CCDS1412
Canonical transcript exons
ENST00000367311 — 2 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001444157 | 201464278 | 201466178 |
| ENSE00001444159 | 201468341 | 201469188 |
Expression profiles
Bgee: expression breadth ubiquitous, 222 present calls, max score 98.79.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.8154 / max 410.9787, expressed in 1597 samples.
FANTOM5 promoters (9 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 16659 | 17.7887 | 1573 |
| 16658 | 6.7143 | 1407 |
| 16660 | 1.8574 | 858 |
| 16654 | 0.4943 | 306 |
| 16657 | 0.3467 | 190 |
| 16653 | 0.2420 | 100 |
| 16656 | 0.2046 | 91 |
| 16655 | 0.0935 | 40 |
| 201872 | 0.0740 | 25 |
Top tissues by expression
270 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| tibial nerve | UBERON:0001323 | 98.79 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 97.71 | gold quality |
| sural nerve | UBERON:0015488 | 97.01 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 96.96 | gold quality |
| lower esophagus | UBERON:0013473 | 96.57 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 96.56 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 96.48 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 96.26 | gold quality |
| stromal cell of endometrium | CL:0002255 | 95.64 | gold quality |
| omental fat pad | UBERON:0010414 | 95.57 | gold quality |
| esophagus | UBERON:0001043 | 95.55 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 95.53 | gold quality |
| peritoneum | UBERON:0002358 | 95.53 | gold quality |
| left coronary artery | UBERON:0001626 | 95.33 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 95.33 | gold quality |
| ascending aorta | UBERON:0001496 | 95.29 | gold quality |
| adipose tissue of abdominal region | UBERON:0007808 | 95.28 | gold quality |
| thoracic aorta | UBERON:0001515 | 95.26 | gold quality |
| spinal cord | UBERON:0002240 | 95.22 | gold quality |
| right coronary artery | UBERON:0001625 | 95.20 | gold quality |
| esophagus mucosa | UBERON:0002469 | 95.14 | gold quality |
| skin of leg | UBERON:0001511 | 95.01 | gold quality |
| coronary artery | UBERON:0001621 | 94.99 | gold quality |
| apex of heart | UBERON:0002098 | 94.85 | gold quality |
| right uterine tube | UBERON:0001302 | 94.84 | gold quality |
| aorta | UBERON:0000947 | 94.76 | gold quality |
| endocervix | UBERON:0000458 | 94.64 | gold quality |
| adipose tissue | UBERON:0001013 | 94.55 | gold quality |
| skin of abdomen | UBERON:0001416 | 94.54 | gold quality |
| popliteal artery | UBERON:0002250 | 94.52 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 13.12 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): TP53
miRNA regulators (miRDB)
78 targeting PHLDA3, 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-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-4481 | 100.00 | 66.42 | 1669 |
| HSA-MIR-4283 | 100.00 | 66.42 | 2097 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-4650-5P | 99.98 | 64.69 | 999 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-6778-3P | 99.96 | 67.29 | 2693 |
| HSA-MIR-4725-3P | 99.96 | 69.53 | 2520 |
| HSA-MIR-6780B-5P | 99.96 | 69.60 | 2562 |
| HSA-LET-7C-3P | 99.95 | 73.42 | 2862 |
| HSA-MIR-185-3P | 99.95 | 67.01 | 1743 |
| HSA-MIR-4271 | 99.88 | 68.32 | 2244 |
| HSA-MIR-4447 | 99.85 | 67.81 | 2900 |
| HSA-MIR-383-3P | 99.85 | 65.84 | 1359 |
| HSA-MIR-6079 | 99.84 | 68.54 | 1170 |
| HSA-MIR-6739-5P | 99.80 | 67.87 | 2806 |
| HSA-MIR-4668-5P | 99.79 | 70.58 | 3782 |
| HSA-MIR-6764-5P | 99.75 | 67.89 | 2304 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-6733-5P | 99.74 | 67.94 | 2759 |
| HSA-MIR-1200 | 99.71 | 70.42 | 1838 |
| HSA-MIR-518A-5P | 99.70 | 69.01 | 2209 |
| HSA-MIR-527 | 99.70 | 69.01 | 2209 |
| HSA-MIR-10394-5P | 99.65 | 66.83 | 1852 |
| HSA-MIR-1205 | 99.65 | 66.76 | 1826 |
| HSA-MIR-378A-5P | 99.65 | 66.33 | 1311 |
| HSA-MIR-1251-3P | 99.64 | 67.21 | 1408 |
| HSA-MIR-6134 | 99.63 | 65.68 | 1537 |
| HSA-MIR-1915-3P | 99.58 | 66.79 | 1988 |
Literature-anchored findings (GeneRIF, showing 11)
- Study identifies PHLDA3 as a p53 target gene that encodes a PH domain-only protein and finds that PHLDA3 competes with the PH domain of Akt for binding of membrane lipids, inhibiting Akt translocation to the cellular membrane and activation. (PMID:19203586)
- findings indicate somatic mutation of PHLDA3 is rare in common cancer types; PHLDA3 expression was lost in 22% of prostate cancers; these results indicate that PHLDA3 are altered in prostate cancers by loss of expression (PMID:21753719)
- Results indicate that tumor suppressor PHLDA3-mediated pathway is important in the development of pancreatic neuroendocrine tumors (PanNETs). (PMID:24912192)
- Low PHLDA3 expression in ESCC may be predictive of tumor recurrence suggesting that Akt activation may be a therapeutic target in ESCCs (PMID:25667479)
- although iPSCs and ESCs share lots of common features, we did not find that PHLDA3 is important to ES cell differentiation. (PMID:28588267)
- Recommendation of long-term and systemic management according to the risk factors in rectal NETs patients. (PMID:30787304)
- Novel Role for Pleckstrin Homology-Like Domain Family A, Member 3 in the Regulation of Pathological Cardiac Hypertrophy. (PMID:31426686)
- Phlda3 regulates beta cell survival during stress. (PMID:31492921)
- Prognostic and predictive value of Pleckstrin homology-like domain, family A family members in breast cancer. (PMID:33179538)
- PHLDA3 exerts an antitumor function in prostate cancer by down-regulating Wnt/beta-catenin pathway via inhibition of Akt. (PMID:34303965)
- PHLDA3 Is an Important Downstream Mediator of p53 in Squamous Cell Carcinogenesis. (PMID:34592332)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | phlda3 | ENSDARG00000037804 |
| mus_musculus | Phlda3 | ENSMUSG00000041801 |
| rattus_norvegicus | Phlda3 | ENSRNOG00000009068 |
Paralogs (2): PHLDA1 (ENSG00000139289), PHLDA2 (ENSG00000181649)
Protein
Protein identifiers
Pleckstrin homology-like domain family A member 3 — Q9Y5J5 (reviewed: Q9Y5J5)
Alternative names: TDAG51/Ipl homolog 1
All UniProt accessions (1): Q9Y5J5
UniProt curated annotations — full annotation on UniProt →
Function. p53/TP53-regulated repressor of Akt/AKT1 signaling. Represses AKT1 by preventing AKT1-binding to membrane lipids, thereby inhibiting AKT1 translocation to the cellular membrane and activation. Contributes to p53/TP53-dependent apoptosis by repressing AKT1 activity. Its direct transcription regulation by p53/TP53 may explain how p53/TP53 can negatively regulate AKT1. May act as a tumor suppressor.
Subcellular location. Cytoplasm. Membrane.
Tissue specificity. Widely expressed with lowest expression in liver and spleen.
Domain organisation. The PH domain binds phosphoinositides with a broad specificity. It competes with the PH domain of AKT1 and directly interferes with AKT1 binding to phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3), preventing AKT1 association to membrane lipids and subsequent activation of AKT1 signaling.
Induction. By p53/TP53; expression is directly activated by TP53. TP53 phosphorylation on ‘Ser-15’ is required to activate the PHLDA3 promoter.
Miscellaneous. PHLDA3 genomic locus is frequently observed in primary lung cancers, suggesting a role in tumor suppression.
Similarity. Belongs to the PHLDA3 family.
RefSeq proteins (1): NP_036528* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001849 | PH_domain | Domain |
| IPR011993 | PH-like_dom_sf | Homologous_superfamily |
| IPR042832 | PHLA1/2/3 | Family |
Pfam: PF00169
UniProt features (5 total): sequence conflict 2, chain 1, domain 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9Y5J5-F1 | 90.81 | 0.81 |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 173 (showing top):
GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE_BY_P53_CLASS_MEDIATOR, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, SP1_Q2_01, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, RICKMAN_METASTASIS_DN, CATTTCA_MIR203, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, BLALOCK_ALZHEIMERS_DISEASE_UP, GROSS_HYPOXIA_VIA_ELK3_UP, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP
GO Biological Process (5): anatomical structure morphogenesis (GO:0009653), intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771), positive regulation of apoptotic process (GO:0043065), negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051898), apoptotic process (GO:0006915)
GO Molecular Function (7): phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547), phosphatidylinositol-5-phosphate binding (GO:0010314), phosphatidylinositol-3-phosphate binding (GO:0032266), phosphatidylinositol-3,4-bisphosphate binding (GO:0043325), phosphatidylinositol-3,5-bisphosphate binding (GO:0080025), phosphatidylinositol phosphate binding (GO:1901981)
GO Cellular Component (3): cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| phosphatidylinositol phosphate binding | 5 |
| phosphatidylinositol bisphosphate binding | 3 |
| anion binding | 2 |
| cellular anatomical structure | 2 |
| developmental process | 1 |
| anatomical structure development | 1 |
| intrinsic apoptotic signaling pathway in response to DNA damage | 1 |
| intrinsic apoptotic signaling pathway by p53 class mediator | 1 |
| apoptotic process | 1 |
| regulation of apoptotic process | 1 |
| positive regulation of programmed cell death | 1 |
| phosphatidylinositol 3-kinase/protein kinase B signal transduction | 1 |
| regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | 1 |
| negative regulation of intracellular signal transduction | 1 |
| programmed cell death | 1 |
| apoptotic signaling pathway | 1 |
| execution phase of apoptosis | 1 |
| phospholipid binding | 1 |
| intracellular anatomical structure | 1 |
| membrane | 1 |
| cell periphery | 1 |
Protein interactions and networks
STRING
497 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| PHLDA3 | AEN | Q8WTP8 | 688 |
| PHLDA3 | PLEK2 | Q9NYT0 | 603 |
| PHLDA3 | PLEK | P08567 | 599 |
| PHLDA3 | KANK3 | Q6NY19 | 537 |
| PHLDA3 | CCNG1 | P51959 | 523 |
| PHLDA3 | ZMAT3 | Q9HA38 | 521 |
| PHLDA3 | CDKN1A | P38936 | 510 |
| PHLDA3 | TP53 | P04637 | 477 |
| PHLDA3 | BBC3 | Q96PG8 | 441 |
| PHLDA3 | EDA2R | Q9HAV5 | 435 |
| PHLDA3 | MDM2 | Q00987 | 423 |
| PHLDA3 | FDXR | P22570 | 421 |
| PHLDA3 | DDIAS | Q8IXT1 | 405 |
| PHLDA3 | BTG2 | P78543 | 397 |
| PHLDA3 | PMAIP1 | Q13794 | 391 |
| PHLDA3 | INKA2 | Q9NTI7 | 391 |
IntAct
102 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CDK2 | PHLDA3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HLA-C | psi-mi:“MI:0914”(association) | 0.350 | |
| PHLDA3 | HSPA8 | psi-mi:“MI:0914”(association) | 0.350 |
| DNAJC25 | TUBAL3 | psi-mi:“MI:0914”(association) | 0.350 |
| PHLDA3 | LRPPRC | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | XPO5 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | ATXN10 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | IPO11 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | ARMC6 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | GCLM | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | PHLDA3 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | DYNLL1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | UFL1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | IPO4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | MAPRE2 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | LBR | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | MYO1A | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | PRPF6 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | SF3B6 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | NUBP2 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | IMMT | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | XPO4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | TFB2M | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | RARS2 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | ARL1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | PDXDC1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | SAAL1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | psi-mi:“MI:0915”(physical association) | 0.000 | |
| PHLDA3 | DYNC1H1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PHLDA3 | COPG2 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (29): DNAAF5 (Affinity Capture-MS), NUP93 (Affinity Capture-MS), PDCD6IP (Affinity Capture-MS), TTC27 (Affinity Capture-MS), NUP205 (Affinity Capture-MS), HNRNPM (Affinity Capture-MS), IPO4 (Affinity Capture-MS), SLC25A12 (Affinity Capture-MS), PDXDC1 (Affinity Capture-MS), LRPPRC (Affinity Capture-MS), ATP5L (Affinity Capture-MS), SSR4 (Affinity Capture-MS), TNPO3 (Affinity Capture-MS), MMS19 (Affinity Capture-MS), XPO5 (Affinity Capture-MS)
ESM2 similar proteins: A1L2W9, B2RQE8, B5XG43, G9CGD6, O08969, O88387, P59113, Q0V987, Q0VC85, Q1KKW7, Q1KKZ1, Q32LP0, Q3UUV5, Q3ZBA3, Q4V7G1, Q503L1, Q53GA4, Q5FVW6, Q5PQT7, Q5R8M5, Q5U597, Q5XGP7, Q5ZL23, Q6P0G8, Q6PG29, Q7Z628, Q7Z6J4, Q80VL0, Q80YS6, Q86UX7, Q86WV1, Q8AW35, Q8BY35, Q8IZC4, Q8K1B8, Q8N556, Q8VH46, Q91ZM9, Q91ZT5, Q925E0
Diamond homologs: A1L2W9, B5XG43, O08969, Q0V987, Q0VC85, Q503L1, Q53GA4, Q5PQT7, Q62392, Q8AW35, Q8WV24, Q9QZA1, Q9WV95, Q9Y5J5
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 98 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 |
|---|---|---|---|
| Translation | 8 | 6.9× | 9e-03 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
15 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 13 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
248 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:201468336:CTTA:C | donor_loss | 1.0000 |
| 1:201468337:TTA:T | donor_loss | 1.0000 |
| 1:201468338:TA:T | donor_loss | 1.0000 |
| 1:201468339:A:AC | donor_gain | 0.9900 |
| 1:201468340:C:CC | donor_gain | 0.9900 |
| 1:201468340:CCTG:C | donor_gain | 0.9900 |
| 1:201468477:TG:T | donor_gain | 0.9900 |
| 1:201466174:CGAAG:C | acceptor_gain | 0.9800 |
| 1:201468347:TG:T | donor_gain | 0.9800 |
| 1:201466177:AGC:A | acceptor_loss | 0.9700 |
| 1:201466178:GCT:G | acceptor_loss | 0.9700 |
| 1:201466179:C:CC | acceptor_gain | 0.9700 |
| 1:201466180:T:G | acceptor_loss | 0.9700 |
| 1:201468339:ACCTG:A | donor_gain | 0.9600 |
| 1:201468340:CCTGC:C | donor_gain | 0.9600 |
| 1:201468343:G:A | donor_gain | 0.9600 |
| 1:201466177:AG:A | acceptor_gain | 0.9400 |
| 1:201468346:TTG:T | donor_gain | 0.9400 |
| 1:201466175:GAAG:G | acceptor_gain | 0.9300 |
| 1:201468339:AC:A | donor_gain | 0.9300 |
| 1:201468340:CC:C | donor_gain | 0.9300 |
| 1:201466176:AAG:A | acceptor_gain | 0.9200 |
| 1:201468340:CCT:C | donor_gain | 0.9100 |
| 1:201469120:C:A | donor_gain | 0.9100 |
| 1:201468341:C:T | donor_gain | 0.9000 |
| 1:201468348:G:T | donor_gain | 0.8700 |
| 1:201466181:G:C | acceptor_loss | 0.8400 |
| 1:201468335:GCT:G | donor_gain | 0.7900 |
| 1:201468518:T:TA | donor_gain | 0.7800 |
| 1:201466176:AAGCT:A | acceptor_gain | 0.7700 |
AlphaMissense
807 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:201468533:A:G | F85S | 1.000 |
| 1:201468505:C:A | W94C | 0.999 |
| 1:201468505:C:G | W94C | 0.999 |
| 1:201468507:A:G | W94R | 0.999 |
| 1:201468507:A:T | W94R | 0.999 |
| 1:201468568:G:C | F73L | 0.999 |
| 1:201468568:G:T | F73L | 0.999 |
| 1:201468569:A:G | F73S | 0.999 |
| 1:201468570:A:G | F73L | 0.999 |
| 1:201468709:C:A | W26C | 0.999 |
| 1:201468709:C:G | W26C | 0.999 |
| 1:201468711:A:G | W26R | 0.999 |
| 1:201468711:A:T | W26R | 0.999 |
| 1:201468494:A:C | I98S | 0.998 |
| 1:201468494:A:G | I98T | 0.998 |
| 1:201468506:C:G | W94S | 0.998 |
| 1:201468710:C:G | W26S | 0.998 |
| 1:201468736:C:A | K17N | 0.998 |
| 1:201468736:C:G | K17N | 0.998 |
| 1:201468531:G:T | R86S | 0.997 |
| 1:201468532:G:C | F85L | 0.997 |
| 1:201468532:G:T | F85L | 0.997 |
| 1:201468534:A:G | F85L | 0.997 |
| 1:201468623:A:G | F55S | 0.997 |
| 1:201468689:A:T | L33H | 0.997 |
| 1:201468700:C:A | K29N | 0.997 |
| 1:201468700:C:G | K29N | 0.997 |
| 1:201468735:G:T | R18S | 0.997 |
| 1:201468472:G:C | F105L | 0.996 |
| 1:201468472:G:T | F105L | 0.996 |
dbSNP variants (sampled 300 via entrez): RS1000190306 (1:201469285 C>G,T), RS1000342724 (1:201464266 T>C), RS1000774888 (1:201470842 C>G), RS1000776142 (1:201464535 G>A,C), RS1000904953 (1:201468166 A>G), RS1001171190 (1:201464080 C>T), RS1001240486 (1:201463875 G>A), RS1001841233 (1:201468776 G>A), RS1002075818 (1:201468088 C>T), RS1002150062 (1:201469065 A>C), RS1002247817 (1:201464972 C>T), RS1002445787 (1:201469462 C>CATCT), RS1003570999 (1:201467417 C>A,T), RS1003674995 (1:201466747 C>A,T), RS1004003582 (1:201469793 G>T)
Disease associations
OMIM: gene MIM:607054 | 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 |
|---|---|---|
| GCST004988_443 | Breast cancer | 4.000000e-13 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
68 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | decreases methylation, increases expression | 5 |
| Aflatoxin B1 | affects expression, increases expression | 4 |
| Cisplatin | increases expression | 3 |
| Cyclosporine | increases expression | 3 |
| sodium arsenite | increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| Tobacco Smoke Pollution | affects expression, increases expression | 2 |
| Cadmium Chloride | decreases expression, increases expression | 2 |
| Particulate Matter | decreases expression, increases abundance, affects cotreatment, increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| tungsten carbide | affects cotreatment, increases expression | 1 |
| chloroacetaldehyde | increases expression | 1 |
| propionaldehyde | increases expression | 1 |
| pirinixic acid | affects binding, decreases expression, increases activity | 1 |
| deoxynivalenol | increases expression | 1 |
| beta-lapachone | increases expression | 1 |
| cobaltous chloride | increases expression | 1 |
| zinc chromate | increases abundance, increases expression | 1 |
| ferrous chloride | decreases expression | 1 |
| cupric chloride | increases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, increases expression, affects cotreatment, decreases expression | 1 |
| polyhexamethyleneguanidine | affects expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| chromium hexavalent ion | increases expression, increases abundance | 1 |
| adefovir dipivoxil | increases expression | 1 |
| pinostrobin | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | increases expression, affects cotreatment | 1 |
| MT19c compound | decreases expression | 1 |
Cellosaurus cell lines
1 cell lines: 1 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_B2AM | Abcam HeLa PHLDA3 KO | Cancer cell line | Female |
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.