pathogenicity-gates 0.5.1

Zero-parameter first-principles pathogenicity prediction via Gate & Channel framework

pathogenicity-gates

Zero-parameter, first-principles Gate & Channel framework for missense variant interpretation

v18 FINAL — 12 channels, 2 Getas, 4 bundled proteins, zero fitted parameters.

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What is this?

pathogenicity-gates is a first-principles framework that classifies missense variants by explicit IF-THEN physical rules — not by regression, not by learned weights, not by latent scores. Each prediction names the specific physical constraint that is violated: a destroyed zinc-binding site, a lost nuclear localization signal, a disrupted coupled-folding interface, a broken proline-directed kinase motif, or any of dozens of other auditable physical gates.

The framework is not a model of biology but a transcription of it: the physical laws have been established by generations of structural biologists, biochemists, and polymer physicists. What this package provides is their translation into IF-THEN rules — one mechanism at a time.

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Quick Start

pip install pathogenicity-gates

Single variant

pathogenicity-gates predict --protein p53 --mutation R175H
# → Pathogenic (Ch02_Zn, Ch03_Core, Ch05_Loop)

Batch prediction

pathogenicity-gates predict-batch --protein p53 --input variants.csv --output results.json

Explain a call

pathogenicity-gates explain --protein p53 --mutation R175H
# → Ch02_Zn: Direct Zn ligand (H179 coordination shell). H→R disrupts...
# → Ch03_Core: Buried charge introduction. R175H places +0.1 charge...
# → Ch05_Loop: Loop anchor disruption at L2/L3 junction...

List bundled proteins

pathogenicity-gates list-proteins
# → p53, kras, tdp43, brca1

Add a new protein

No code modification required. Supply a YAML annotation file + a PDB or AlphaFold structure:

pathogenicity-gates predict --protein my_protein --config my_protein.yaml --structure my_protein.pdb --mutation G12V

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4 Principles

1. Thresholds are derived from physics, not from data fitting. Ramachandran angles, van der Waals radii, pKa values — all from textbooks.

2. Gates are IF-THEN, not continuous scores. Binary decisions. No regression. No weighting. Parameters = ZERO.

3. Missed variants = missing Gate, not a threshold problem. When a pathogenic variant escapes, it names the next IF-THEN to be written.

4. Incidental closures → physical Geta exception, not threshold relaxation. When a gate expansion creates false positives on legitimately tolerated variants, a Geta (post-closure exception rule) is added. Getas must be protein-independent, rescue zero ClinVar Pathogenic variants, and generalize to any protein where the primary gate applies.

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Architecture: 12 Channels + 2 Getas

The framework evaluates each variant across independent channels. A variant is predicted Pathogenic if any gate in any channel closes: n_closed ≥ 1.

A second hierarchical layer (Geta) reverses specific closures whose physical condition predicts tolerance. Gates and Getas operate on disjoint variant populations — there is no coverage-vs-tolerance trade-off.

Structured-domain channels (from 3D coordinates)

Channel	Physical target	Input
Ch01_DNA	DNA-contact disruption	Side-chain → DNA distance (1TSR)
Ch02_Zn	Metal coordination (Zn²⁺)	Cα → Zn distance, charge logic
Ch03_Core	Symmetry-complete core integrity	Burial, volume, charge, H-bond, aromaticity, sulfur
Ch04_SS	Secondary-structure incompatibility	Helix/β propensity, backbone strain
Ch05_Loop	Ramachandran endpoint constraints	Pro→X, Gly→X, loop anchors
Ch06_PPI	Protein-protein interface	Union of 16 p53 complex structures (66 residues)
Ch07_PTM	PTM-site chemistry + proximity	31 UniProt sites, MECE structured/IDR split
Ch08_Oligomer	Tetramer-interface disruption	Exposure asymmetry, rigid multi-chain hub
Ch09_SaltBridge	Surface salt-bridge networks	Charged pairs within 10 Å at surface

IDR-specific channels (1D, no coordinates)

Channel	Physical target	Mechanism
Ch10_SLiM	Short linear motif disruption	Gate C (6-partner coupled folding), PPII, NLS, aromatic anchor, CT-reg
Ch11_IDR_Pro	Context-dependent Pro→X	PPII, SLiM interior, SLiM boundary, PTM-proximal, isolated
Ch12_IDR_Gly	IDR glycine constraint	G→X: side-chain introduction constrains required backbone freedom

Geta layer (post-closure exceptions)

Geta	Acts on	Condition	Rescue
Geta_VI	Ch03_Core	V↔I: both β-branched aliphatic, differ by one CH₂	0 Path rescued
Geta_IDR_PTM	Ch07_PTM (IDR)	Charge-preserving K↔R, R↔H, S↔T within ±1 of PTM site	0 Path rescued

Transferability

Tier	Channels	Input requirement
UNIVERSAL	Ch07, Ch10, Ch11, Ch12, Geta_VI, Geta_IDR_PTM	Sequence + annotation only
ADAPTABLE	Ch03, Ch04, Ch05, Ch06, Ch09	PDB or AlphaFold (pLDDT > 70)
SPECIFIC	Ch01 (DNA-bound), Ch02 (metal site)	Target-specific structural input

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Performance (p53, v18 FINAL)

Metric	Value
Variants evaluated	1,369
Sensitivity	84.5%
PPV	89.1%
Core domain sensitivity	90.9%
Hotspots captured	9/9
VUS reclassified	407/578 (70.4%)
Mol-adjusted PPV	92.2%
Fitted parameters	0

Per-region sensitivity

Region	Gate type	Sensitivity	PPV
Core (94–289)	3D	90.9%	94.7%
Tet (325–356)	3D	67.5%	71.1%
TAD1 (1–40)	1D	92.1%	81.5%
TAD2 (41–61)	1D	76.2%	71.4%
PRD (62–93)	1D	66.7%	76.9%
Linker (290–324)	1D	41.9%	65.0%
CTD (357–393)	1D	70.6%	70.6%

Hotspot capture (9/9)

Variant	Channels closed
R175H	Ch02_Zn, Ch03_Core, Ch05_Loop
C176F	Ch02_Zn, Ch03_Core, Ch05_Loop
H179R	Ch02_Zn
Y220C	Ch03_Core
G245S	Ch03_Core, Ch05_Loop
R248W	Ch01_DNA, Ch05_Loop, Ch06_PPI
R249S	Ch03_Core, Ch05_Loop
R273H	Ch01_DNA, Ch03_Core
R280K	Ch01_DNA, Ch03_Core

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Cross-protein validation

The same channels — without modification — capture the dominant pathogenic mechanisms in three additional cancer-relevant proteins. Where they fail, the failure names a specific gate yet to be written.

KRAS

• Captured: G12V/D/C, G13D (Ch03_Core, Ch04_SS); K117N, A146T (Ch03_Core); K184Q (IDR charge logic)
• Gate yet to be written: Q61H/L → catalytic / cofactor channel (transition-state geometry around Mg²⁺/GTP)

TDP-43

• Captured: G294A, G295V, G348C (Ch12_IDR_Gly); A315T, A382T (Ch10 PPII spacer β-branch); N382D, N390D (Ch10 IDR charge)
• Gate yet to be written: M337V → aggregation / LLPS channel (aromatic spacing, charge patterning)

BRCA1

• RING domain: C61G, C64R, T37R (Ch02_Zn analog, Ch03_Core)
• BRCT buried: V1696L, K1702N, A1708E, M1775R, C1697R (Ch03_Core)
• BRCT phospho-pocket: S1655F, R1699Q, R1699W, S1715R (Gate C with ABRAXAS1 + BACH1 + CtIP; PDBs 1T29, 1T15, 1Y98)

Gate C architectural portability

The "union of partner faces + non-conservative filter" pattern is protein-independent:

p53 TAD  × {MDM2, CBP TAZ2, CBP TAZ1, NCBD, p300 TAZ2}  → 59 union residues, 6 PDBs
BRCA1 BRCT × {ABRAXAS1, BACH1, CtIP}                     → working Gate C, 3 PDBs

Replace the partner set → Gate C works. No logic change required.

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Gate Specifications

Channel 1: DNA-contact disruption (Ch01_DNA)

Side-chain heavy-atom to DNA heavy-atom distance from 1TSR (Chain B → Chains E/F).

Gate 1.1 — Direct contact (d < 3.5 Å):
  IF wt ∈ {R,K} AND mt ∉ {R,K}  → CLOSED
  IF ΔHB_capacity ≥ 1            → CLOSED
  IF |ΔQ| > 0.5                  → CLOSED

Gate 1.2 — Proximal contact (3.5 ≤ d < 6.0 Å):
  IF ΔQ < -0.5                    → CLOSED
  IF wt ∈ {R,K} AND mt ∉ {R,K,H} → CLOSED
  IF ΔHB_capacity ≥ 2             → CLOSED

Channel 2: Zn coordination (Ch02_Zn)

Layered cascade model. Direct ligands: C176, H179, C238, C242.

Gate 2.1 — Direct coordination (Layer 1):
  IF pos ∈ {176, 238, 242, 179} → CLOSED

Gate 2.2 — Electrostatic environment (d_Cα_Zn < 8.0 Å):
  IF d_Cα_Zn < 8.0 AND |ΔQ| > 0.5 → CLOSED

Channel 3: Core integrity (Ch03_Core)

Symmetry-complete packing logic with burial-dependent thresholds.

Tier S (benign = 0):

S1: X→Gly  — Ramachandran freedom explosion (buried)
S2: S...π  — Chalcogen interaction loss (M/C → non-M/C, aromatic neighbor)
S3: Met sulfur network — Zn seismic isolation (M → non-M/C, n_sul ≥ 3)
S4: β-branch loss in β-strand — interlock collapse (V/I/T → non-V/I/T, buried β)
S5: polar→hydrophobic — H-bond partner loss (deeply buried)

Tier A (symmetric pairs):

• Volume: cavity ⇄ steric clash
• Charge: loss ⇄ introduction ⇄ sign reversal
• Hydrophobicity: hydro→polar ⇄ polar→hydro
• H-bond: loss ⇄ gain
• Aromatic: gain in buried sites
• Surface hydrophobic exposure
• Electrostatic keystone (≥4 charged neighbors)

Geta_VI: V↔I substitutions at buried β-branched positions are rescued — both rotamers fit the same cavity.

Channel 4: Secondary structure (Ch04_SS)

Helix: ΔP_helix < -0.30, backbone strain < -0.5, Pro disruption
Beta:  ΔP_beta < -0.30 (buried), Pro loss in β-structure

Channel 5: Structured loop/Pro/Gly (Ch05_Loop)

Pro→X in structured regions → CLOSED (Tier S, position-independent)
Gly→X in L2/L3 loops → CLOSED
X→Pro in helices/strands → CLOSED
Loop anchor large perturbation → CLOSED

Channel 6: PPI interface (Ch06_PPI)

Union of 16 p53 complex structures (66 interface residues in core domain).

IF n_pdbs ≥ 3 AND physicochemical_change     → CLOSED
IF min_d < 3.5 AND charge/hydro_change       → CLOSED
IF PPI_nb ≥ 5 AND charge/volume_change       → CLOSED

Channel 7: PTM logic (Ch07_PTM) — MECE split

31 UniProt P04637 sites. Structured and IDR sub-gates have different proximity radii.

7a: Direct PTM site hit — any domain
7b: Proximity ±2 — structured domains (OR logic: charge OR volume)
7c: Proximity ±1 — IDR (OR logic: charge OR volume)
7d: [S/T]-P proline-directed kinase motif — Pro ring = recognition element

Confirmed [S/T]-P motifs:

Phosphosite	Pro	Kinase	Validation
S33	P34	CDK5/CDK7	P34A/T/R/S = all Path (4/4)
S46	P47	CDK5/DYRK2/HIPK2	P47T/R = Path (2/2)
S315	P316	CDK1/CDK2	P316L/S = Path (2/2)

Geta_IDR_PTM: Charge-preserving substitutions (K↔R, R↔H, S↔T) within ±1 of a PTM site in IDR are rescued — disordered backbone absorbs local geometry, charge and H-bond chemistry preserved.

Channel 8: Oligomer interface (Ch08_Oligomer)

Tetramerization domain (2J0Z). Exposure asymmetry + rigid multi-chain hub logic.

Rigid hub (Tier S): IF n_chains_contacted ≥ 2 → CLOSED

Channel 9: Surface salt bridge (Ch09_SaltBridge)

IF burial < 0.5 AND opposite_charge_partner < 10 Å AND |ΔQ| > 0.5 → CLOSED

Channel 10: SLiM motif disruption (Ch10_SLiM)

Sub-gate	Mechanism	Key variants
Gate C	Coupled folding: 6-partner union face (1YCR/5HPD/5HOU/2L14/2K8F/2MZD; 59 residues). Non-conservative substitution at union-face residue → CLOSED	F19X, W23X, L26X, D49H, I50T
Gate A	PPII incompatibility: aromatic intro in PRD → CLOSED	X→W/F/Y in PRD
Gate A2	PPII spacer β-branch: {A,G}→{V,I,T} → CLOSED	A69V, A83V, A86V
Gate NLS	NLS charge loss: basic→neutral → CLOSED	R379C, K373N
Gate ARO	Aromatic anchor loss in binding pocket → CLOSED	W53L, F54L
Gate CT_reg	C-terminal regulatory charge pattern disruption → CLOSED	D391N, T387R

Channel 11: IDR proline (Ch11_IDR_Pro)

Context-dependent Pro→X in disordered regions. P72 (rs1042522) explicitly excluded.

1. PRD polyproline motif → CLOSED (PPII structure)
2. SLiM interior → CLOSED (binding interface geometry)
3. SLiM boundary N-cap (±2) → CLOSED (Pro lacks amide H → helix breaker)
4. PTM proximity (±2) → CLOSED (backbone constrains enzyme access)
5. Isolated IDR Pro → OPEN (no defined functional context)

Channel 12: IDR glycine (Ch12_IDR_Gly)

IF is_IDR AND wt == G AND mt ≠ G → CLOSED

In disordered regions, backbone freedom is the function. G→X introduces a side chain → constrains the conformational space required for coupled folding, flexible linker behavior, or PTM accessibility. The absence of structure is the information.

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Symmetry verification (all pairs confirmed)

Forward	Reverse	Status
Cavity	Steric clash	✅
Gly→X	X→Gly	✅
Pro→X	X→Pro	✅
Charge loss	Charge intro	✅
Charge flip	(self-symmetric)	✅
Hydro→polar	Polar→hydro	✅
H-bond loss	H-bond gain	✅
Aromatic loss	Aromatic gain	✅
β-branch loss	≈ steric	✅
PPII compat→incompat	Gate A	✅
PPII spacer→β-branch	Gate A2	✅

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Tier S summary

Structured domains (benign = 0)

#	Gate	Physics
1	X→Gly (Ch03)	Ramachandran freedom explosion
2	Pro→X (Ch05)	Ramachandran constraint release
3	β-branch loss in β-strand (Ch03)	Interlock collapse
4	Surface salt bridge (Ch09)	Electrostatic zipper disruption
5	Polar→hydrophobic buried (Ch03)	H-bond partner loss
6	Met sulfur network (Ch03)	Chalcogen network / Zn seismic isolation
7	Rigid hub ≥2 chains (Ch08)	Tetramer-interface rigidity

IDR hard constraints (1D, no coordinates)

#	Gate	Physics
8	Coupled folding (Ch10 Gate C)	6-partner union face: non-conservative subst. → CLOSED
9	[S/T]-P kinase motif (Ch07d)	Pro ring loss → kinase substrate unrecognizable
10	PPII spacer β-branch (Ch10 A2)	{A,G}→{V,I,T} restricts φ-angle
11	IDR Gly→X (Ch12)	Side-chain introduction constrains required backbone freedom
12	NLS charge loss (Ch10 NLS)	Basic→neutral abolishes nuclear import signal

Geta layer (post-closure exceptions)

#	Geta	Physics	ClinVar Path rescued
13	Geta_VI	V↔I in buried β-branched positions	0
14	Geta_IDR_PTM	Charge-preserving K↔R, R↔H, S↔T within ±1 of PTM in IDR	0

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Next gates to be written

Where the framework fails, it names what to add:

Category	Example	Gate needed	Data required
Conservative substitutions	D21E, D49E	Partner-pocket fingerprint	Additional complex structures
PRD non-Pro positions	A78V, T81I	SH3-like binding pocket	SH3-PRD complex structure
Linker orphans	N310K, Q317H	Dynamics / persistence	NMR or cryo-EM dynamics
CTD 360–362 cluster	G360V, S362N	SLiM boundary extension	Mutational scanning
Isolated IDR Pro→X	P4R, P58R	Polymer compaction	SAXS / smFRET measurements
KRAS Q61H/L	Q61H	Catalytic / cofactor channel	Transition-state geometry (Mg²⁺/GTP)
TDP-43 M337V	M337V	Aggregation / LLPS channel	Aromatic spacing, charge patterning

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Repository structure

pathogenicity_gates/          # Installable Python package
  ├── channels/               # Channel and Geta logic
  ├── data/                   # Bundled per-protein annotations
  │   ├── p53/                # YAML + PDB + partner_face.json (59 residues)
  │   ├── kras/
  │   ├── tdp43/
  │   └── brca1/
  └── cli.py                  # Command-line interface

tests/                        # pytest suite
Result/                       # Per-variant prediction outputs and run logs
supplementary/                # Machine-readable CSV/JSON (S1–S6 Tables)
paper_markdown/               # Design rationale and gate specifications

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AlphaFold compatibility

• ADAPTABLE channels (Ch03, Ch04, Ch05, Ch06, Ch09): accept AlphaFold structures with pLDDT > 70.
• UNIVERSAL channels (Ch07, Ch10, Ch11, Ch12, Getas): operate from sequence and annotation alone — AlphaFold confidence is irrelevant.
• Gate C extension: AlphaFold-Multimer predictions can supply partner-complex interfaces where experimental structures are unavailable.

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Reproducibility

The framework is deterministic and rule-based. The archived Zenodo release and PyPI package v0.5.1 provide the version-locked snapshot:

pip install pathogenicity-gates==0.5.1
pathogenicity-gates predict-batch --protein p53 \
    --input <bundled tp53_clinvar_missense.csv> \
    --output v18_final_results.json

Any change in outputs is traceable to a changed input file, an altered gate definition, or a scope correction — never to stochastic optimization.

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Citation

If you use this framework, please cite:

M.Iizumi. A zero-parameter first-principles gate framework for full-length TP53 missense variant interpretation. PLOS Computational Biology (under review). 2026.

Zenodo DOI: 10.5281/zenodo.19214741

ORCID: 0009-0007-0755-403X

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Acknowledgments

AI tools were used in a limited, supervised manner to support framework development, manuscript drafting, code inspection, and hypothesis exploration. Specific contributions: No AI tool was used as a substitute for scientific judgment. All framework definitions, analyses, and interpretations were reviewed and approved by the author.

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License

MIT

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"If you can turn a classifier into a puzzle game, it's not a black box."

Credits: Ramachandran (1963) · Flory (1969) · Barlow & Thornton (1983) · Burley & Petsko (1985)