# PHOSPHO2

> Gene · canonical: https://sugi.bio/atlas/gene/PHOSPHO2/
> Atlas v1.12.2 · generated 2026-10-13T13:32:47+00:00

## Summary

**PHOSPHO2** (phosphatase, orphan 2, HGNC:28316) is a protein-coding gene on chromosome 2q31.1, encoding **Pyridoxal phosphate phosphatase PHOSPHO2** (Q8TCD6). Phosphatase that has high activity toward pyridoxal 5'-phosphate (PLP).

Predicted to enable phosphatase activity.

*Source: [NCBI Gene 493911](https://www.ncbi.nlm.nih.gov/gene/493911) — automated summary from GO annotations (Alliance of Genome Resources).*

**At a glance**

- **GWAS associations:** 1
- **Clinical variants (ClinVar):** 32 total
- **GTEx eGene:** eQTL in 47 tissues, sQTL in 39 (q < 0.05)
- **Constraint (gnomAD):** pLI 0.00 (LoF-tolerant), LOEUF 1.30 (unconstrained)
- **MANE Select transcript:** `NM_001008489`




## Identifiers

### Gene identifiers

| Field | Value |
| --- | --- |
| HGNC ID | HGNC:28316 |
| Approved symbol | PHOSPHO2 |
| Name | phosphatase, orphan 2 |
| Location | 2q31.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | MGC22679 |
| Ensembl gene | ENSG00000144362 |
| Ensembl biotype | protein_coding |
| Entrez | 493911 |

## Gene structure

### Transcript identifiers

**Ensembl transcripts: 35** — 34 protein_coding, 1 protein_coding_CDS_not_defined

**MANE Select:** `ENST00000359744`

**Transcript support level (Ensembl TSL; 1 = fully mRNA-supported):** TSL 1: 1, TSL 2: 2, TSL 3: 5

`ENST00000359744`, `ENST00000438710`, `ENST00000438838`, `ENST00000449906`, `ENST00000476919`, `ENST00000616481`, `ENST00000616524`, `ENST00000617738`, `ENST00000857416`, `ENST00000857417`, `ENST00000857418`, `ENST00000857419`, `ENST00000857420`, `ENST00000857421`, `ENST00000857422`, `ENST00000857423`, `ENST00000857424`, `ENST00000931227`, `ENST00000931228`, `ENST00000931229`, `ENST00000931230`, `ENST00000931231`, `ENST00000931232`, `ENST00000931233`, `ENST00000931234`, `ENST00000931235`, `ENST00000931236`, `ENST00000931237`, `ENST00000931238`, `ENST00000931239`, `ENST00000931240`, `ENST00000961207`, `ENST00000961208`, `ENST00000961209`, `ENST00001144211`

**RefSeq mRNA: 5** — MANE Select: `NM_001008489`
`NM_001008489`, `NM_001199285`, `NM_001199286`, `NM_001199287`, `NM_001199288`

**CCDS:** `CCDS33319`

#### Canonical transcript exons

`ENST00000359744` — 4 exons

| Exon | Start | End |
| --- | --- | --- |
| ENSE00001413182 | 169700946 | 169701708 |
| ENSE00001466648 | 169694469 | 169694622 |
| ENSE00003515401 | 169697361 | 169697531 |
| ENSE00003520671 | 169695215 | 169695247 |

### Expression profiles

**Bgee:** expression breadth **ubiquitous**, 237 present calls, max score 96.30.

**FANTOM5 (CAGE):** breadth **tissue_specific**, TPM avg 0.0250 / max 4.5835, expressed in 15 samples.

**Highest expression (Bgee):** secondary oocyte, oocyte, sperm, male germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad.

#### Genetic regulation across tissues (GTEx eQTL / sQTL)

PHOSPHO2 is an **eGene** in GTEx v10 — its expression is genetically regulated (eQTL) in **47** tissues and its splicing (sQTL) in **39** (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant's alternative allele.

showing 20 of 86 significant tissue × QTL associations:

| Tissue | QTL | q-value | Slope | Lead variant |
| --- | --- | --- | --- | --- |
| Testis | sqtl | 2.1e-93 | -3.08 | 2:169694622:G:A |
| Nerve Tibial | sqtl | 1.7e-74 | -2.18 | 2:169694622:G:A |
| Artery Tibial | sqtl | 3.4e-74 | -2.22 | 2:169694622:G:A |
| Thyroid | sqtl | 1.2e-73 | -2.25 | 2:169694622:G:A |
| Adipose Subcutaneous | sqtl | 1.9e-71 | -2.20 | 2:169694622:G:A |
| Cells Cultured fibroblasts | sqtl | 1.5e-56 | -1.97 | 2:169694622:G:A |
| Breast Mammary Tissue | sqtl | 1.9e-54 | -2.27 | 2:169694622:G:A |
| Muscle Skeletal | sqtl | 4.8e-53 | -1.74 | 2:169694622:G:A |
| Colon Transverse | sqtl | 4.9e-42 | -2.08 | 2:169694622:G:A |
| Skin Sun Exposed Lower leg | sqtl | 1.4e-41 | -1.67 | 2:169694622:G:A |
| Esophagus Muscularis | sqtl | 2.4e-41 | -2.24 | 2:169694622:G:A |
| Colon Sigmoid | sqtl | 7.0e-40 | -2.25 | 2:169694622:G:A |
| Adipose Visceral Omentum | sqtl | 1.5e-37 | -1.96 | 2:169694622:G:A |
| Skin Not Sun Exposed Suprapubic | sqtl | 6.7e-37 | -1.80 | 2:169694622:G:A |
| Artery Tibial | eqtl | 1.9e-36 | -0.55 | 2:169701721:T:C |
| Artery Aorta | sqtl | 5.1e-35 | -1.95 | 2:169694622:G:A |
| Nerve Tibial | eqtl | 1.8e-33 | -0.56 | 2:169712014:C:T |
| Thyroid | eqtl | 2.6e-33 | -0.59 | 2:169699317:TC:T |
| Colon Transverse | eqtl | 3.3e-29 | -0.50 | 2:169706187:T:TCA |
| Adipose Subcutaneous | eqtl | 5.1e-29 | -0.41 | 2:169712014:C:T |

#### FANTOM5 promoters

2 alternative TSS:

| Promoter ID | TPM avg | Samples expressed |
| --- | --- | --- |
| 23564 | 5.7217 | 1471 |
| 23566 | 0.0250 | 15 |

#### Top tissues by expression

showing 100 of 249 tissues by Bgee expression score (0-100, higher = more expressed):

| Tissue | Anatomy ID | Expression score | Quality |
| --- | --- | --- | --- |
| secondary oocyte | CL:0000655 | 96.30 | gold quality |
| oocyte | CL:0000023 | 96.21 | gold quality |
| sperm | CL:0000019 | 94.25 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 89.33 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 86.95 | gold quality |
| corpus epididymis | UBERON:0004359 | 86.54 | gold quality |
| caput epididymis | UBERON:0004358 | 86.45 | gold quality |
| tibia | UBERON:0000979 | 85.69 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 84.81 | gold quality |
| left testis | UBERON:0004533 | 84.42 | gold quality |
| right testis | UBERON:0004534 | 84.06 | gold quality |
| testis | UBERON:0000473 | 83.61 | gold quality |
| bronchial epithelial cell | CL:0002328 | 82.38 | gold quality |
| cauda epididymis | UBERON:0004360 | 82.18 | gold quality |
| bronchus | UBERON:0002185 | 81.39 | gold quality |
| calcaneal tendon | UBERON:0003701 | 80.91 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 80.43 | gold quality |
| rectum | UBERON:0001052 | 80.18 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 80.11 | gold quality |
| mammary duct | UBERON:0001765 | 80.03 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 79.68 | gold quality |
| mammary gland | UBERON:0001911 | 79.57 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 79.20 | gold quality |
| duodenum | UBERON:0002114 | 79.19 | gold quality |
| islet of Langerhans | UBERON:0000006 | 78.82 | gold quality |
| right uterine tube | UBERON:0001302 | 78.77 | gold quality |
| prostate gland | UBERON:0002367 | 78.76 | gold quality |
| thyroid gland | UBERON:0002046 | 78.63 | gold quality |
| adipose tissue | UBERON:0001013 | 78.48 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 78.41 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 78.40 | gold quality |
| body of pancreas | UBERON:0001150 | 78.34 | gold quality |
| adult organism | UBERON:0007023 | 78.25 | gold quality |
| jejunal mucosa | UBERON:0000399 | 78.18 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 78.00 | gold quality |
| pancreas | UBERON:0001264 | 77.86 | gold quality |
| left ovary | UBERON:0002119 | 77.83 | gold quality |
| parietal pleura | UBERON:0002400 | 77.59 | gold quality |
| ventricular zone | UBERON:0003053 | 77.51 | gold quality |
| transverse colon | UBERON:0001157 | 77.50 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 77.41 | gold quality |
| popliteal artery | UBERON:0002250 | 77.40 | gold quality |
| tibial artery | UBERON:0007610 | 77.38 | gold quality |
| colon | UBERON:0001155 | 77.25 | gold quality |
| right ovary | UBERON:0002118 | 77.20 | gold quality |
| large intestine | UBERON:0000059 | 77.17 | gold quality |
| pancreatic ductal cell | CL:0002079 | 77.05 | silver quality |
| ovary | UBERON:0000992 | 76.86 | gold quality |
| colonic mucosa | UBERON:0000317 | 76.83 | gold quality |
| intestine | UBERON:0000160 | 76.81 | gold quality |
| ganglionic eminence | UBERON:0004023 | 76.66 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 76.65 | gold quality |
| pituitary gland | UBERON:0000007 | 76.57 | gold quality |
| minor salivary gland | UBERON:0001830 | 76.53 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 76.51 | gold quality |
| adenohypophysis | UBERON:0002196 | 76.51 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 76.46 | gold quality |
| ectocervix | UBERON:0012249 | 76.43 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 76.37 | gold quality |
| cortical plate | UBERON:0005343 | 76.37 | gold quality |
| body of uterus | UBERON:0009853 | 76.36 | gold quality |
| aorta | UBERON:0000947 | 76.16 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 76.16 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 76.07 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 76.07 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 76.04 | gold quality |
| lower esophagus | UBERON:0013473 | 76.02 | gold quality |
| visceral pleura | UBERON:0002401 | 75.93 | gold quality |
| endocervix | UBERON:0000458 | 75.51 | gold quality |
| gastrocnemius | UBERON:0001388 | 75.43 | gold quality |
| parotid gland | UBERON:0001831 | 75.42 | silver quality |
| small intestine Peyer's patch | UBERON:0003454 | 75.30 | gold quality |
| skin of hip | UBERON:0001554 | 75.28 | gold quality |
| left coronary artery | UBERON:0001626 | 75.27 | gold quality |
| left uterine tube | UBERON:0001303 | 75.25 | gold quality |
| adipose tissue of abdominal region | UBERON:0007808 | 75.19 | gold quality |
| tibial nerve | UBERON:0001323 | 75.16 | gold quality |
| small intestine | UBERON:0002108 | 75.14 | gold quality |
| endometrium | UBERON:0001295 | 75.04 | gold quality |
| adrenal tissue | UBERON:0018303 | 75.03 | gold quality |
| mucosa of stomach | UBERON:0001199 | 74.96 | gold quality |
| ascending aorta | UBERON:0001496 | 74.87 | gold quality |
| mouth mucosa | UBERON:0003729 | 74.79 | gold quality |
| right coronary artery | UBERON:0001625 | 74.76 | gold quality |
| urinary bladder | UBERON:0001255 | 74.74 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 74.73 | gold quality |
| thoracic aorta | UBERON:0001515 | 74.72 | gold quality |
| peritoneum | UBERON:0002358 | 74.64 | gold quality |
| omental fat pad | UBERON:0010414 | 74.64 | gold quality |
| muscle of leg | UBERON:0001383 | 74.61 | gold quality |
| gall bladder | UBERON:0002110 | 74.60 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 74.33 | gold quality |
| ileal mucosa | UBERON:0000331 | 74.23 | gold quality |
| uterus | UBERON:0000995 | 74.20 | gold quality |
| body of stomach | UBERON:0001161 | 74.17 | gold quality |
| right atrium auricular region | UBERON:0006631 | 74.12 | gold quality |
| coronary artery | UBERON:0001621 | 74.01 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 73.90 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 73.84 | gold quality |
| female reproductive system | UBERON:0000474 | 73.67 | gold quality |

#### Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

| Experiment | Marker? | Max mean expression |
| --- | --- | --- |
| [E-ANND-3](https://www.ebi.ac.uk/gxa/sc/experiments/E-ANND-3) | yes | 3.44 |

#### HPA expression

RNA tissue specificity: **Low tissue specificity**

showing 60 of 80 HPA tissues / cells by nTPM:

| Tissue / cell | Axis | nTPM | Protein (IHC) |
| --- | --- | --- | --- |
| Frontal cortex | tissue | 24.4 |  |
| Caudate putamen | tissue | 23.0 |  |
| Cerebellum | tissue | 18.1 | medium |
| Putamen | tissue | 14.2 |  |
| Prostate | tissue | 12.2 | medium |
| Choroid plexus | tissue | 12.1 |  |
| Testis | tissue | 11.8 | medium |
| Basal ganglia | tissue | 11.2 | low |
| Cerebral cortex | tissue | 10.9 | low |
| Somatosensory cortex | tissue | 10.9 |  |
| Occipital cortex | tissue | 10.9 |  |
| Ventral forebrain | tissue | 10.8 |  |
| Olfactory bulb | tissue | 10.5 |  |
| Hippocampal formation | tissue | 10.3 |  |
| Entorhinal cortex | tissue | 10.3 |  |
| Prefrontal cortex | tissue | 10.0 |  |
| Retrosplenial and cingulate cortex | tissue | 10.0 |  |
| Breast | tissue | 9.9 | medium |
| Motor cortex | tissue | 9.8 |  |
| Septum | tissue | 9.8 |  |
| Thalamus | tissue | 9.7 |  |
| Pons | tissue | 9.6 |  |
| Retrosplenial cortex | tissue | 9.6 |  |
| Temporal cortex | tissue | 9.6 |  |
| Thyroid gland | tissue | 9.2 | medium |
| Midbrain | tissue | 9.1 |  |
| Insular cortex | tissue | 9.1 |  |
| Superior colliculi | tissue | 8.9 |  |
| Amygdala | tissue | 8.8 |  |
| Hypothalamus | tissue | 8.6 |  |
| Substantia nigra | tissue | 8.3 |  |
| Periaqueductal gray | tissue | 8.3 |  |
| Salivary gland | tissue | 8.0 | medium |
| Nucleus accumbens | tissue | 7.3 |  |
| Medulla oblongata | tissue | 7.3 |  |
| Locus coeruleus | tissue | 7.2 |  |
| Spinal cord | tissue | 7.2 |  |
| Parathyroid gland | tissue | 6.8 | medium |
| Retina | tissue | 6.7 |  |
| Hippocampus | tissue | 6.7 | not detected |
| Small intestine | tissue | 6.0 | medium |
| Duodenum | tissue | 6.0 | medium |
| Corpus callosum | tissue | 6.0 |  |
| Fallopian tube | tissue | 5.6 | medium |
| Rectum | tissue | 5.5 | medium |
| Colon | tissue | 5.5 | medium |
| Kidney | tissue | 5.2 | medium |
| Postcentral gyrus | tissue | 5.0 |  |
| Endometrium 1 | tissue | 4.9 | medium |
| Pancreas | tissue | 4.8 | medium |
| Adipose tissue | tissue | 4.7 | low |
| Stomach 1 | tissue | 4.5 | medium |
| Seminal vesicle | tissue | 4.5 | medium |
| Cervix | tissue | 4.4 | medium |
| Pituitary gland | tissue | 4.3 |  |
| Ovary | tissue | 4.2 | not detected |
| Epididymis | tissue | 4.0 | medium |
| Gallbladder | tissue | 3.7 | medium |
| Liver | tissue | 3.4 | not detected |
| Skin 1 | tissue | 3.3 | medium |

**Brain sub-regions (HPA Brain Atlas):** detected in 192; highest nTPM — Cerebellar cortex (12.7), Vermis (12.5), Flocculonodular lobe (11.9), Arcuate nucleus (10.0), Subiculum (9.4).

### Regulation

**Is transcription factor: no**

### Functional genomics

**gnomAD constraint:** pLI 6.28e-05, LOEUF 1.3, missense Z 1.03 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). [gnomAD](https://gnomad.broadinstitute.org/)

**Regional missense constraint (gnomAD RMC):** no regional variation along `ENST00000359744` — one region, missense o/e 0.87.

### Literature-anchored findings (GeneRIF, showing 1)

- Models of PHOSPHO2 and PHOSPHO1 suggest subtle differences in the charge distributions around the putative substrate entry site and in the location of potential H-bond donors. (PMID:16054448)

### Cross-species orthologs

**5 orthologs**

| Organism | Symbol | Gene ID |
| --- | --- | --- |
| danio_rerio | phospho2 | ENSDARG00000102202 |
| mus_musculus | Phospho2 | ENSMUSG00000027088 |
| rattus_norvegicus | Phospho2 | ENSRNOG00000007979 |
| drosophila_melanogaster | CG14212 | FBGN0031045 |
| drosophila_melanogaster | CG12237 | FBGN0031048 |

**Paralogs (1):** PHOSPHO1 (ENSG00000173868)

#### Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara's model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions' gene symbols aren't in biobtree yet, so each row shows the UniProt accession.

| Organism | UniProt | Identity | Method |
| --- | --- | --- | --- |
| Bos taurus | [Q2KI06](https://www.uniprot.org/uniprotkb/Q2KI06/entry) | 85.5% | Diamond |
| Arabidopsis thaliana | [Q9FZ62](https://www.uniprot.org/uniprotkb/Q9FZ62/entry) | 77.0% | Diamond |
| Xenopus tropicalis | [Q66KD6](https://www.uniprot.org/uniprotkb/Q66KD6/entry) | 62.5% | Diamond |
| Gallus gallus | [O73884](https://www.uniprot.org/uniprotkb/O73884/entry) | 61.1% | Diamond |

### Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

| Symbol | Type | Entrez |
| --- | --- | --- |
| PHOSPHO2-KLHL23 | protein-coding | 100526832 |
| [CFAP210](/atlas/gene/CFAP210/) | protein-coding | 129881 |
| [FASTKD1](/atlas/gene/FASTKD1/) | protein-coding | 79675 |
| [PPIG](/atlas/gene/PPIG/) | protein-coding | 9360 |
| [KLHL23](/atlas/gene/KLHL23/) | protein-coding | 151230 |
| [KLHL41](/atlas/gene/KLHL41/) | protein-coding | 10324 |

<a id="protein-Q8TCD6"></a>

## Protein

### Protein identifiers

**Pyridoxal phosphate phosphatase PHOSPHO2** — `Q8TCD6` (reviewed: Q8TCD6)

**All UniProt accessions (4):** `C9J4G2`, `C9JD35`, `C9JZQ7`, `Q8TCD6`

#### UniProt curated annotations — [full annotation on UniProt →](https://www.uniprot.org/uniprotkb/Q8TCD6/entry)

**Function.** Phosphatase that has high activity toward pyridoxal 5'-phosphate (PLP). Also active at much lower level toward pyrophosphate, phosphoethanolamine (PEA), phosphocholine (PCho), phospho-l-tyrosine, fructose-6-phosphate, p-nitrophenyl phosphate, and h-glycerophosphate.

**Similarity.** Belongs to the HAD-like hydrolase superfamily. PHOSPHO family.

**RefSeq proteins (5):** `NP_001008489`*, `NP_001186214`, `NP_001186215`, `NP_001186216`, `NP_001186217`  (*=MANE)

#### Domains & families (InterPro)

| ID | Name | Type |
| --- | --- | --- |
| IPR006384 | HAD_hydro_PyrdxlP_Pase-like | Family |
| IPR016965 | Pase_PHOSPHO-typ | Family |
| IPR023214 | HAD_sf | Homologous_superfamily |
| IPR036412 | HAD-like_sf | Homologous_superfamily |

**Pfam:** `PF06888`

#### Catalyzed reactions (Rhea)

- pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate *(RHEA:20533)*

**UniProt features (9 total):** binding site 5, active site 2, chain 1, sequence variant 1

### Structure

#### Predicted structure (AlphaFold)

| Model | pLDDT | Fraction very-high |
| --- | --- | --- |
| AF-Q8TCD6-F1 | 96.04 | 0.94 |

### Human Protein Atlas

**Protein class:** Enzymes, ENZYME proteins, Hydrolases, Metabolic proteins, Predicted intracellular proteins

**Protein evidence:** Evidence at protein level

**Subcellular location (HPA, imaging):** vesicles; nucleoplasm

**Antibody reliability (HPA):** IH uncertain · IF approved

### Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. *Source: UniProtKB sequence features.*

#### Catalytic / active sites (2)

| Position | Role |
| --- | --- |
| 8 | nucleophile |
| 10 | proton donor |

#### Ligand- & substrate-binding residues (5)

| Position | Role |
| --- | --- |
| 8 | Mg(2+) |
| 10 | Mg(2+) |
| 19 | substrate |
| 99 | substrate |
| 179 | Mg(2+) |

## Function

### Pathways and Gene Ontology

#### Reactome pathways

**0 curated (TAS)** of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

**MSigDB gene sets: 52** (showing top):
`GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS`, `GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY`, `JOHNSTONE_PARVB_TARGETS_3_DN`, `WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D`, `FORTSCHEGGER_PHF8_TARGETS_DN`, `GOMF_PHOSPHATASE_ACTIVITY`, `WNT_UP.V1_DN`, `FOXJ2_TARGET_GENES`, `FOXN3_TARGET_GENES`, `ZNF711_TARGET_GENES`, `CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2`, `GSE14769_UNSTIM_VS_120MIN_LPS_BMDM_UP`, `GSE14769_UNSTIM_VS_240MIN_LPS_BMDM_DN`, `GSE15930_STIM_VS_STIM_AND_IFNAB_48H_CD8_T_CELL_DN`, `GSE17721_CPG_VS_GARDIQUIMOD_24H_BMDC_DN`

**GO Molecular Function (5):**
phosphatase activity (GO:0016791), pyridoxal phosphatase activity (GO:0033883), metal ion binding (GO:0046872), protein binding (GO:0005515), hydrolase activity (GO:0016787)

#### GO top-level categories

5 GO namespaces:

| Category | Terms |
| --- | --- |
| phosphoric ester hydrolase activity | 1 |
| phosphatase activity | 1 |
| cation binding | 1 |
| binding | 1 |
| catalytic activity | 1 |

### Protein interactions and networks

#### STRING

showing 15 of 378 interactions by confidence (×1000):

| Protein A | Protein B | Partner UniProt | Score |
| --- | --- | --- | --- |
| PHOSPHO2 | KLHL23 | Q8NBE8 | 571 |
| PHOSPHO2 | ZNF487 | B1APH4 | 540 |
| PHOSPHO2 | PALD1 | Q9ULE6 | 534 |
| PHOSPHO2 | OXLD1 | Q5BKU9 | 524 |
| PHOSPHO2 | A6NDT3 | A6NDT3 | 470 |
| PHOSPHO2 | A0A0A6YYL6 | A0A0A6YYL6 | 460 |
| PHOSPHO2 | NT5M | Q9NPB1 | 444 |
| PHOSPHO2 | ZSCAN9 | O15535 | 441 |
| PHOSPHO2 | CFAP210 | Q0VFZ6 | 435 |
| PHOSPHO2 | METTL9 | Q9H1A3 | 362 |
| PHOSPHO2 | IWS1 | Q96ST2 | 358 |
| PHOSPHO2 | TMEM69 | Q5SWH9 | 356 |
| PHOSPHO2 | INPP5K | Q9BT40 | 355 |
| PHOSPHO2 | SNF8 | Q96H20 | 349 |
| PHOSPHO2 | C18orf32 | Q8TCD1 | 344 |

#### IntAct

Human interaction partners of PHOSPHO2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

11 partners by confidence:

| Partner | Interaction type | MIscore | Records |
| --- | --- | --- | --- |
| NAB2 | physical association | 0.720 | 6 |
| ATP5PF | physical association | 0.560 | 5 |
| TSEN15 | physical association | 0.560 | 5 |
| WASHC3 | physical association | 0.560 | 5 |
| C1QTNF2 | physical association | 0.560 | 3 |
| FLNA | physical association | 0.560 | 3 |
| GKAP1 | physical association | 0.560 | 3 |
| JPH3 | physical association | 0.560 | 3 |
| VHL | physical association | 0.560 | 3 |
| SIGLEC5 | association | 0.530 | 2 |
| SPARC | physical association | 0.400 | 1 |

**BioGRID (14 interactions; top human partners by supporting records):** DNTTIP1 (Affinity Capture-MS; 2 records), NAB2 (Two-hybrid; 2 records), SIGLEC5 (Affinity Capture-MS; 2 records), ATP5J (Two-hybrid), C1QTNF2 (Two-hybrid), CCDC53 (Two-hybrid), CPNE4 (Affinity Capture-MS), DDX39A (Affinity Capture-RNA), FLNA (Two-hybrid), GKAP1 (Two-hybrid), TSEN15 (Two-hybrid)

## Disease & clinical

### Genetic variants

**Variant evidence for PHOSPHO2:** [32 ClinVar records](#clinvar) (0 pathogenic / likely pathogenic); [1 GWAS association](#gwas-assoc).

#### ClinVar

32 variants total. Per-class counts are floors (≥ shown; pagination cap):

| Classification | Count (floor) |
| --- | --- |
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 31 |
| Likely benign | 1 |
| Benign | 0 |

#### SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 19 predictions of 468):

| Position(s) | Effect | Δscore | Sites |
| --- | --- | --- | --- |
| 2:169695248–169695249 | donor_loss | 0.9700 | 5 |
| 2:169698246 | donor_gain | 0.9700 |  |
| 2:169695213–169695214 | acceptor_loss | 0.9600 | 6 |
| 2:169695249 | donor_loss | 0.9600 |  |
| 2:169695204 | acceptor_loss | 0.9400 |  |
| 2:169695252 | donor_loss | 0.9300 |  |
| 2:169698481 | donor_gain | 0.9300 |  |
| 2:169695252 | donor_loss | 0.9000 |  |
| 2:169695212 | acceptor_loss | 0.8900 |  |
| 2:169698246 | donor_gain | 0.8900 |  |

#### AlphaMissense

399 missense substitutions predicted likely pathogenic (of 1,621 scored), across 113 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
| --- | --- | --- | --- |
| D8 | 8 | 0.965 | 0.989 |
| D183 | 8 | 0.957 | 0.977 |
| D10 | 8 | 0.950 | 0.975 |
| D179 | 8 | 0.923 | 0.972 |
| D99 | 8 | 0.919 | 0.974 |
| D19 | 8 | 0.912 | 0.958 |
| N150 | 8 | 0.840 | 0.971 |
| M48 | 8 | 0.747 | 0.887 |
| C152 | 7 | 0.947 | 0.971 |
| K153 | 7 | 0.937 | 0.997 |
| W225 | 7 | 0.918 | 0.978 |
| W44 | 7 | 0.897 | 0.960 |
| C185 | 7 | 0.888 | 0.970 |
| C147 | 7 | 0.876 | 0.958 |
| F9 | 7 | 0.863 | 0.968 |
| N101 | 7 | 0.856 | 0.971 |
| N124 | 7 | 0.850 | 0.947 |
| C144 | 7 | 0.842 | 0.898 |
| F104 | 7 | 0.829 | 0.923 |
| N182 | 7 | 0.823 | 0.939 |

### HPA cancer prognostics

**RNA cancer specificity:** Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

| Cancer | Prognostic | p-value |
| --- | --- | --- |
| Kidney Renal Clear Cell Carcinoma (TCGA) | favorable | 2.61e-08 |
| Liver Hepatocellular Carcinoma (TCGA) | unfavorable | 9.29e-06 |
| Rectum Adenocarcinoma (TCGA) | favorable | 0.000354 |

### Disease associations

**OMIM:** gene `` | disease phenotypes: 

#### GWAS associations

1 associations:

| Study | Trait | p-value |
| --- | --- | --- |
| GCST005184_8 | Common carotid intima-media thickness in HIV infection | 5e-6 |

## Drugs & pharmacology

### Drug and pharmacology data

**Is drug target: no**

**PharmGKB:** 1 entry (CPIC guideline: no)

#### CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

| Chemical | Actions (top 5) | PubMed papers |
| --- | --- | --- |
| trichostatin A | affects cotreatment, decreases expression | 3 |
| Dexamethasone | increases expression, affects cotreatment | 2 |
| Nickel | decreases expression | 2 |
| Cyclosporine | decreases expression | 2 |
| methylmercuric chloride | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | affects cotreatment, increases expression | 1 |
| potassium chromate(VI) | increases expression | 1 |
| 4-aminophenylarsenoxide | affects binding, decreases reaction | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Arsenic Trioxide | affects binding, decreases reaction | 1 |
| Acetaminophen | increases expression | 1 |
| Cisplatin | decreases expression | 1 |
| Coumestrol | decreases expression | 1 |
| Indomethacin | increases expression, affects cotreatment | 1 |
| Quercetin | affects expression | 1 |
| Dihydrotestosterone | increases expression | 1 |
| Urethane | decreases expression | 1 |
| Vanadates | decreases expression | 1 |
| 1-Methyl-3-isobutylxanthine | affects cotreatment, increases expression | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
| Copper Sulfate | decreases expression | 1 |
| Magnetite Nanoparticles | increases methylation | 1 |

#### Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

## Related Atlas pages

*No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.*