Clival chordoma research
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Skull base anatomy

Agent report for Kya, 8 September 2026, for her partner's question "which areas are affected right now". Every clinical and anatomical claim carries a PMID verified through NCBI E-utilities on 8 September 2026, or a URL fetched the same day. Web search was unavailable and Radiopaedia blocked automated access, so the anatomy is cited to StatPearls chapters (NCBI Bookshelf) and, for two structures, Wikipedia; the tumour behaviour is cited to the surgical and neuro-ophthalmology literature. Where I am reasoning from anatomy rather than quoting a study I say so. The patient's imaging is known only from the Treliske discharge summary as relayed, not from the images. No survival figures, by rule.

The report as relayed: 3.8 cm mass centred on the clivus, extensive skull base bone destruction, extension into the prepontine cistern, partial encasement of the basilar artery, involvement of the cavernous sinus abutting both cavernous carotids, right third and fourth nerve involvement. Not mentioned as involved: optic nerves or chiasm, pituitary, temporal lobes, brainstem substance.

1. The clivus and its neighbours

The clivus is the sloping plate of bone behind the sphenoid sinus, formed by the basisphenoid and basiocciput fused at the sphenooccipital synchondrosis; it runs from the dorsum sellae above to the foramen magnum below, and "the pons sits on the basilar surface of the clivus" with the basilar artery between them; the abducens nerve tracks along it (https://en.wikipedia.org/wiki/Clivus_(anatomy)). Chordoma arises from notochord remnants in this bone and, on CT, "typically appears as a centrally located, well-circumscribed, expansile soft-tissue mass that arises from the clivus with associated extensive lytic bone destruction" (Erdem 2003, Radiographics, PMID 12853676). Six directions:

2. The cranial nerves that pass the clivus

III, oculomotor. Leaves the midbrain between the posterior cerebral and superior cerebellar arteries, runs in the roof and lateral wall of the cavernous sinus, then through the superior orbital fissure. It lifts the lid, moves the eye up, down and in, and constricts the pupil. Failure: ptosis, eye resting "down and out", and a dilated pupil if the pupil fibres are hit; those fibres sit on the surface of the nerve, so compression tends to involve the pupil while small-vessel ischaemia spares it (StatPearls, CN III Palsy, https://www.ncbi.nlm.nih.gov/books/NBK526112/; StatPearls CN3, https://www.ncbi.nlm.nih.gov/books/NBK537126/). The patient's right ptosis since July is a third nerve sign; whether the right pupil is large and sluggish is worth asking.

IV, trochlear. The thinnest nerve with the longest intracranial course; runs in the lateral wall of the cavernous sinus above VI; supplies the superior oblique, which depresses and intorts the eye. Failure: vertical or diagonal double vision worse looking down and in (reading, stairs), the affected eye riding slightly high, head tilt to the opposite shoulder (StatPearls CN4, https://www.ncbi.nlm.nih.gov/books/NBK537244/). It is hard to test when III is also out; the report records it, so the radiologist saw tumour at the nerve.

V, trigeminal. Arises from the side of the pons, crosses the prepontine cistern to the ganglion in Meckel's cave at the petrous apex, then splits: V1 (forehead, cornea, upper nose) and V2 (cheek, upper lip, upper teeth, lower nose, palate) run in the cavernous sinus lateral wall; V3 (jaw, lower lip, tongue sensation, chewing muscles) leaves by the foramen ovale and never enters the sinus. Failure: numbness or pain in the territory, lost corneal reflex, jaw deviation or masseter wasting if V3 (StatPearls CN5, https://www.ncbi.nlm.nih.gov/books/NBK482283/). V3 sparing localises to the sinus (NBK532976). The patient's right facial pain of over a year is the oldest sign; in petroclival tumours, trigeminal pain means Meckel's cave is reached and abducens paresis means the cavernous sinus around Dorello's canal is reached (Kawase 1996, PMID 8786827). Photophobia is carried by a retino-thalamic pathway that converges on trigeminovascular pain neurons (Noseda and Burstein 2011, PMID 21467933; 2013, PMID 23891892), so it fits her trigeminal pain and is not by itself a pressure sign.

VI, abducens, and Dorello's canal. Nucleus in the dorsal pons; exits at the pontomedullary junction, climbs the clivus in the prepontine cistern, "crosses the upper edge of the tip of the petrous part of the temporal bone towards the clivus within a fibrous sheath called Dorello's canal", runs lateral to the carotid in the cavernous sinus, and supplies the lateral rectus. Failure: esotropia, horizontal double vision worse at distance and looking toward the weak side (NBK430711; StatPearls, Abducens Nerve Palsy, https://www.ncbi.nlm.nih.gov/books/NBK482177/). Dorello's canal is roofed by Gruber's petrosphenoidal ligament (https://en.wikipedia.org/wiki/Dorello%27s_canal; Kshettry 2013, PMID 23451716); the nerve's petroclival segment sits in a dural sleeve about 9.5 mm long and 1.5 mm wide (Ozveren 2007, PMID 17297359) after a cisternal run averaging 13 mm up the clivus (Ono 2004, PMID 15090355). Two consequences. First, both sixth nerves lie against the clivus, one each side of the midline, so a midline tumour can reach either or both directly; in 113 Pittsburgh skull base chordomas, 34 presented with a sixth nerve deficit and the nerve "was most commonly radiographically abutted at the prepontine cistern and Dorello's canal" (Muthiah 2025, J Neurosurg, PMID 39823590). Second, because the nerve is anchored in the canal and has the second longest intracranial course, it is "prone to stretching when intracranial pressure is increased", and bilateral palsy is the classic false localising sign of raised pressure (NBK430711; Larner 2003, JNNP, PMID 12640051; Lepore 2002, PMID 12441839); it has resolved with CSF diversion in hydrocephalus (Tsuburaya 2024, PMID 39640382). So the patient's new left sixth nerve sign of 6 Sep has two candidate causes, tumour crossing the midline in the prepontine cistern, or raised pressure; only fundi and imaging separate them, which is why it was treated as a red flag. VI also pairs with XII in Godtfredsen syndrome, whose commonest cause is a clival lesion (Ishihara 2026, PMID 40369741); tongue deviation would be the tell.

3. The pons and the lower cranial nerves

The pons carries the corticospinal tracts to the limbs, the ascending sensory tracts, the pontine nuclei that link to the cerebellum, the nuclei of V to VIII, and the reticular formation that keeps a person awake; its blood comes mostly from basilar branches. Damage gives weakness, incoordination, cranial nerve signs, and in severe compression altered consciousness, respiratory compromise or a locked-in state (StatPearls, Brainstem, https://www.ncbi.nlm.nih.gov/books/NBK544297/). Signs of pontine compression to watch: weakness or clumsiness of an arm or leg, unsteady gait, slurred speech, trouble swallowing, facial weakness, body numbness, and any drop in alertness not explained by medicines. Chordomas can indent the pons without invading it; "brainstem invasion" is a distinct, higher grade (PMID 29126120), and the Treliske report describes cistern extension, not brainstem change.

If tumour grows down toward the foramen magnum, the lower nerves are at risk. Jugular foramen involvement (IX, X, XI) gives hoarseness, dysphagia, loss of gag, palate deviation and a drooping shoulder; adding XII makes Collet-Sicard syndrome (NBK549871). A twelfth nerve palsy shows as the tongue deviating toward the weak side on protrusion, with wasting and clumsy speech (StatPearls CN12, https://www.ncbi.nlm.nih.gov/books/NBK532869/). Dysphagia was presenting in 14 percent of 50 clival chordomas (PMID 25594191). Nothing in the patient's history points here.

4. The vessels

The basilar artery runs up the front of the pons in the prepontine cistern and supplies the pons through perforators, the cerebellum and, at its top, the midbrain and occipital lobes; occlusion gives vertigo, double vision, slurred speech, swallowing difficulty, ataxia, weakness of one or both sides and reduced consciousness, which is "the hallmark of basilar artery occlusion" (StatPearls, Basilar Artery Infarct, https://www.ncbi.nlm.nih.gov/books/NBK551854/). Partial encasement matters mainly for surgery. In Paris, 24 chordomas encasing the vertebrobasilar system by 180 degrees or more had a gross total resection rate of 13 percent against 42 percent in matched controls, with no difference in new deficits or CSF leak, and the authors' rule was to let adherence guide the resection and leave a small piece of tumour rather than risk the artery (Champagne 2020, PMID 32324880). Chordomas tend to displace rather than fully encase the carotid (Goel 1995, PMID 8561033). Carotid injury occurred in 0.3 percent of 2,015 Pittsburgh endonasal cases, but 3 of the 7 injuries were in chordoma or chondrosarcoma (2 percent of 142), usually at the paraclival segment, and none caused a stroke (Gardner 2013, PMID 23695646); in Bologna, 65 clival chordomas gave 2.5 percent carotid injuries, coiled without deficit (Zoli 2018, PMID 28409727). Stroke from the tumour itself is rare at presentation and the report describes abutment and partial encasement, not narrowing. Clinical reasoning: the vessel question is a surgical planning question (CT angiogram done; balloon occlusion testing is sometimes used, Gay 1995, PMID 7791978), not a day-to-day risk at home.

5. CSF and pressure

CSF leaves the fourth ventricle through the foramina of Luschka and Magendie into the basal cisterns, the prepontine cistern among them, then over the brain to the arachnoid granulations; obstruction at the fourth ventricle outlets or foramen magnum, or blockage of the cisterns, causes hydrocephalus (StatPearls, Hydrocephalus, https://www.ncbi.nlm.nih.gov/books/NBK560875/). Adult signs: headache worse in the morning or lying flat, nausea, "explosive" vomiting, drowsiness, blurred or double vision, papilloedema, failure of upgaze, unsteady gait, confusion, incontinence (NBK560875; StatPearls, Increased Intracranial Pressure, https://www.ncbi.nlm.nih.gov/books/NBK482119/). Hydrocephalus is uncommon in clival chordoma at presentation but reported (PMID 31226887). The Southampton CT of 5 Sep showed no acute change, which covers ventricle size, but it predates the left sixth nerve sign.

6. Structures next door that the report does not describe as involved

Optic nerves and chiasm. The chiasm sits above the pituitary and diaphragma sellae (StatPearls, Bitemporal Hemianopsia, https://www.ncbi.nlm.nih.gov/books/NBK545213/). Compression from below takes the outer (temporal) half of each field first, then acuity, then the optic nerves and cavernous sinus; perimetry is the most sensitive test (Foroozan 2003, PMID 14615635). Practical checks: cover each eye and read small print; compare the redness of a red object between eyes (colour desaturation is an early optic nerve sign, clinical reasoning); bumping into things at the sides. In Boston, visual loss was more typical of chondrosarcoma than chordoma (PMID 8420385). The patient has diplopia from the motor nerves but no reported acuity or field loss.

Pituitary and hypothalamus. Compression of gland or stalk gives hypopituitarism (fatigue, postural hypotension, cold intolerance, amenorrhoea), raised prolactin, and, if the stalk or posterior pituitary is damaged, vasopressin deficiency (diabetes insipidus) with polyuria, thirst and a rising sodium; the screen is morning cortisol, TSH and free T4, prolactin, LH, FSH, oestradiol, IGF-1 and sodium (StatPearls, Hypopituitarism, https://www.ncbi.nlm.nih.gov/books/NBK470414/; AVP Disorder, https://www.ncbi.nlm.nih.gov/books/NBK470458/). Endocrinology saw the patient on 3 Sep for this; the page 1 bloods are the missing piece. Watch for large volumes of pale urine with thirst, faintness on standing, and a missed period.

Temporal lobes. The medial temporal lobe lies above the cavernous sinus and petrous apex, inside the dura, and the report does not mention it. Temporal lobe seizures classically begin with an aura: a rising feeling in the stomach, deja vu, fear, "olfactory or gustatory hallucinations", depersonalisation, then staring, lip-smacking or fidgeting automatisms, a spell of 30 seconds to 2 minutes, and confusion afterwards (StatPearls, Mesial TLE, https://www.ncbi.nlm.nih.gov/books/NBK554432/; Focal Impaired Awareness Seizure, https://www.ncbi.nlm.nih.gov/books/NBK519030/). The patient's two spaced-out or unreal spells, the "off meat" phantom smell and the metallic taste are the symptoms that overlap. Honest weighing: (a) the tumour is extradural and central; reaching the temporal lobe needs a lateral dural breach the report does not describe, so a structural cause is possible but unsupported; (b) morphine lists confusion, altered mood and hallucination as recognised effects and impairs alertness (Morphine 10 mg/5 ml SmPC, https://www.medicines.org.uk/emc/product/3427/smpc); opioid-induced neurotoxicity (hypersomnolence, hallucinations, delirium, myoclonus) ran at 6.4 to 38 percent in palliative cohorts (Le Bihan 2026, PMID 41876211); gabapentin lists somnolence, dizziness and ataxia as very common and confusion, emotional lability, abnormal thinking and amnesia as common (Neurontin SmPC, https://www.medicines.org.uk/emc/product/3195/smpc); (c) phantom smell affects 6.5 percent of US adults over 40, more in younger women, and rises with the number of prescribed medicines (Bainbridge 2018, PMID 30128498; 2020, PMID 33343789); (d) a blocked right nostril with metallic taste points to local nasal or nasopharyngeal irritation from anterior tumour, which distorts smell and taste without brain involvement (clinical reasoning from PMID 19193749). One spell preceded gabapentin, which weakens (b) for that episode but not for morphine. The discriminators are a stereotyped sequence each time, a stomach-rising or deja vu warning, lip-smacking or picking movements, unresponsiveness witnessed by her partner, and confusion afterwards. Any of those makes it a seizure question for the team (EEG, and the temporal lobes looked at specifically on the next MRI). Without them, medicines and the nose remain more likely.

7. How clival chordoma usually presents

Headache and neck pain (33.2 percent) and diplopia (29 percent) were the commonest initial symptoms in 238 skull base chordomas at Beijing Tiantan, mean age 38 (Wang 2017, J Neurosurg, PMID 28059654). In San Francisco, 50 clival chordomas of mean diameter 3.3 cm presented with headache in 38 percent, diplopia in 36 percent and dysphagia in 14 percent (Jahangiri 2015, PMID 25594191). In Boston, 52 percent of 48 chordoma patients had an ocular symptom first; "headache and diplopia from an insidious abducens nerve palsy was most common", abducens palsy occurred in 46 percent, diplopia was intermittent at first in 42 percent, reflecting "the vulnerability of the abducens nerves at that site" (Volpe 1993, PMID 8420385). In Pittsburgh, 30 percent presented with a sixth nerve deficit and 68 percent recovered at least partly after surgery, 83 percent when the deficit was partial (PMID 39823590). StatPearls lists headache, facial numbness, sixth nerve palsy, ptosis, visual loss and dysphagia (https://www.ncbi.nlm.nih.gov/books/NBK430846/). The patient's order, a year of trigeminal pain, then ptosis, then diplopia, then a contralateral sixth, is the expected sequence for a tumour growing from the upper and middle clivus into the right cavernous sinus and then across the prepontine cistern; the third nerve going before the sixth suggests the bulk sat higher and more lateral on the right than average (clinical reasoning; upper clivus tumours present with oculomotor paresis, PMID 8786827).

8. Map of the patient's signs to structures

Sign Most likely structure Confidence Note
Right trigeminal-distribution pain, over a year Right V at Meckel's cave or cavernous sinus lateral wall (V1 or V2) Definite for nerve V; site likely Oldest sign; ask which divisions are numb; V3 involvement would mean spread below the sinus (PMID 8786827, NBK482283)
Right ptosis since July Right III in cavernous sinus roof or lateral wall Definite (report names III) Pupil size and reaction tell whether the trunk is compressed (NBK526112)
Diplopia since late August, worst on left gaze Right III, with right IV Definite (report names both) Right eye cannot adduct; vertical component from IV (NBK537244)
New left eye cannot fully abduct, 6 Sep Left VI in prepontine cistern or Dorello's canal, or raised pressure Likely structural; pressure possible Needs fundi and imaging to separate (NBK430711, PMID 12640051, PMID 39823590)
Photophobia Trigeminal pain pathway Likely Not a localising sign on its own; also listed under raised pressure (PMID 21467933, NBK482119)
Left "sinus" pain, three times on 7 Sep Left V1 or V2, or sphenoid sinus mucosa Possible New left-sided sensory symptom; alongside the left VI it suggests midline crossing; report to team
Blocked right nostril Anterior extension into sphenoid sinus or nasopharynx Possible Nasal endoscopy answers it (PMID 19193749)
Metallic taste and "off meat" phantom smell Nasal or nasopharyngeal irritation, medicines, or (less likely) temporal lobe Possible, cause uncertain See section 6 (PMID 30128498, PMID 33343789, SmPCs)
Two spaced-out or unreal spells Morphine with or without gabapentin; temporal lobe irritation is the alternative to exclude Possible, medicines more likely Stereotyped aura, automatisms, unresponsiveness or after-confusion would change this (NBK554432, PMID 41876211)
Drowsiness Morphine and gabapentin Likely Very common with gabapentin (Neurontin SmPC); watch for drowsiness that outlasts the dose pattern, which is a pressure or brainstem sign (NBK560875)

Signs that would show involvement of structures not yet reported

9. Plain-language summary for her partner

The clivus is the sloping bone at the centre of the skull base. In front of it are the sphenoid sinus and the back of the nose. Behind it, across a thin layer of fluid, are the basilar artery and the pons, the part of the brainstem that carries the wires to the arms and legs and keeps a person awake. On each side is the cavernous sinus, a pocket of veins that the carotid artery and four nerves pass through: the third (lifts the lid, moves the eye), the fourth (moves the eye down and in), the sixth (moves the eye outward) and the two upper branches of the fifth (feeling in the forehead, cheek and upper teeth). Above sit the pituitary gland and, above that, the optic nerves. Below are the nerves for swallowing, voice, shoulder and tongue.

The patient's tumour sits in that bone and has grown sideways into the right cavernous sinus and backward into the fluid space in front of the brainstem. That explains every sign in order: the year of right facial pain (fifth nerve), the droopy right lid (third), the double vision (third and fourth), and now the left eye not turning fully outward (the left sixth nerve, which runs up the clivus on the other side of the midline; raised pressure inside the head can also do this, which is why it needs an examination and a scan). The light sensitivity comes with the pain pathway. The blocked nostril fits the front edge of the tumour.

The report does not say the tumour has reached the optic nerves, the pituitary, the brainstem itself or the temporal lobe. Each has its own warning signs, listed above, and none of them is present. The spaced-out spells and the strange smell and taste are most likely from the morphine and gabapentin, and from the nose, but a seizure from the temporal lobe cannot be ruled out from the story alone. If a spell ever comes with a warning feeling, lip-smacking, the patient not responding, or confusion afterwards, that is a seizure question and the team should be told the same day.

The wrapped artery is a surgical planning problem, not a day-to-day danger. Surgeons leave a sliver of tumour on a vessel rather than risk it.

Sources

PMIDs: 12853676, 19193749, 29126120, 36930271, 32324880, 25594191, 8786827, 21467933, 23891892, 23451716, 17297359, 15090355, 39823590, 12640051, 12441839, 39640382, 40369741, 8561033, 23695646, 28409727, 7791978, 31226887, 14615635, 8420385, 41876211, 30128498, 33343789, 28059654.

Bookshelf and web: StatPearls NBK430711, NBK537244, NBK482283, NBK537126, NBK526112, NBK532976, NBK545213, NBK551529, NBK470414, NBK470458, NBK544297, NBK551854, NBK532869, NBK549871, NBK560875, NBK482119, NBK482177, NBK554432, NBK519030, NBK430846 (all at https://www.ncbi.nlm.nih.gov/books/); Wikipedia pages Clivus (anatomy), Cavernous sinus, Dorello's canal, Subarachnoid cisterns, Hypoglossal canal, Sphenoid sinus (fetched 8 Sep 2026); Neurontin 300 mg SmPC (emc product 3195) and Morphine 10 mg/5 ml Oral Solution SmPC (emc product 3427).

Research thread 17 · source file em-research/17-skull-base-anatomy-map.md · last edited 08 September 2026