Human Phenotype Ontology 
Grandparent Node:
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Constitutional symptom (HP:0025142)help
Parent Node:
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Abnormal musculoskeletal physiology (HP:0011843)help
Parent Node:
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Pain (HP:0012531)help
..Starting node
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Bone pain (HP:0002653)help
Term ID: 2653
Name: Bone pain
Synonym: Bone pain
Definition: An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone.
Comments:
Reference: HP:0002653
Genes and Diseases:
 
       Child Nodes:

 Sister Nodes: 
..expandAbdominal pain (HP:0002027) help
..expandAllodynia (HP:0012533) help
..expandAnal pain (HP:0500005) help
..expandAnkle pain (HP:0030840) help
..expandArthralgia (HP:0002829) help
..expandBack pain (HP:0003418) help
..expandChest pain (HP:0100749) help
..expandChronic pain (HP:0012532) help
..expandCostochondral pain (HP:0006649) help
..expandEar pain (HP:0030766) help
..expandElbow pain (HP:0030835) help
..expandEpigastric pain (HP:0410019) help
..expandFinger pain (HP:0030837) help
..expandFlank pain (HP:0030157) help
..expandFoot pain (HP:0025238) help
..expandGroin pain (HP:0031520) help
..expandHip pain (HP:0030838) help
..expandJaw pain (HP:0040264) help
..expandKnee pain (HP:0030839) help
..expandLimb pain (HP:0009763) help
..expandMandibular pain (HP:0200025) help
..expandMyalgia (HP:0003326) help
..expandNeck pain (HP:0030833) help
..expandOcular pain (HP:0200026) help
..expandScrotal pain (HP:0030155) help
..expandShoulder pain (HP:0030834) help
..expandToe pain (HP:0030841) help
..expandVulvodynia (HP:0030943) help
..expandWrist pain (HP:0030836) help
InputHPO IDHPO termDistanceGeneGene id entrezHGNC IDDiseaseIdDiseaseNameFrequencyOnsetHGMD variantsClinVar variants
 
HPO disease - gene - phenotype typical associations:
 
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0002653HP:0002653Bone pain0AGXT CL E G H189341OMIM:259900Hyperoxaluria, primary, type I.260
HP:0002653HP:0002653Bone pain0AP2S1 CL E G H1175565OMIM:600740Hypocalciuric hypercalcemia, familial, type III.6
HP:0002653HP:0002653Bone pain0ASXL1 CL E G H17102318318ORPHA:98850Aggressive systemic mastocytosisHP:0040282 - Frequent145
HP:0002653HP:0002653Bone pain0ASXL1 CL E G H17102318318ORPHA:98849Systemic mastocytosis with associated hematologic neoplasmHP:0040283 - Occasional145
HP:0002653HP:0002653Bone pain0ATP7B CL E G H540870ORPHA:905Wilson diseaseHP:0040281 - Very frequent315
HP:0002653HP:0002653Bone pain0BCOR CL E G H5488020893ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional101
HP:0002653HP:0002653Bone pain0CBL CL E G H8671541ORPHA:98850Aggressive systemic mastocytosisHP:0040282 - Frequent317
HP:0002653HP:0002653Bone pain0CCND1 CL E G H5951582ORPHA:29073Multiple myelomaHP:0040282 - Frequent1
HP:0002653HP:0002653Bone pain0CDC73 CL E G H7957716783ORPHA:99880Hyperparathyroidism-jaw tumor syndromeHP:0040283 - Occasional169
HP:0002653HP:0002653Bone pain0CDC73 CL E G H7957716783ORPHA:143Parathyroid carcinomaHP:0040283 - Occasional169
HP:0002653HP:0002653Bone pain0CLCN5 CL E G H11842023OMIM:300009Dent disease 1.112
HP:0002653HP:0002653Bone pain0CLCN5 CL E G H11842023OMIM:300554Hypophosphatemic rickets, X-linked recessive.112
HP:0002653HP:0002653Bone pain0CLCN7 CL E G H11862025ORPHA:53Albers-Schönberg osteopetrosisHP:0040281 - Very frequent102
HP:0002653HP:0002653Bone pain0CLCN7 CL E G H11862025ORPHA:667Autosomal recessive malignant osteopetrosisHP:0040281 - Very frequent102
HP:0002653HP:0002653Bone pain0CYP19A1 CL E G H15882594ORPHA:91Aromatase deficiencyHP:0040281 - Very frequent60
HP:0002653HP:0002653Bone pain0CYP27B1 CL E G H15942606ORPHA:289157Hypocalcemic vitamin D-dependent ricketsHP:0040281 - Very frequent41
HP:0002653HP:0002653Bone pain0CYP27B1 CL E G H15942606OMIM:264700Vitamin D hydroxylation-deficient rickets, type 1A.41
HP:0002653HP:0002653Bone pain0CYP2R1 CL E G H12022720580ORPHA:289157Hypocalcemic vitamin D-dependent ricketsHP:0040281 - Very frequent5
HP:0002653HP:0002653Bone pain0CYP2R1 CL E G H12022720580OMIM:600081Vitamin D hydroxylation-deficient rickets, type 1B.5
HP:0002653HP:0002653Bone pain0DKK1 CL E G H229432891ORPHA:85193Idiopathic juvenile osteoporosisHP:0040281 - Very frequent
HP:0002653HP:0002653Bone pain0DMP1 CL E G H17582932ORPHA:289176Autosomal recessive hypophosphatemic ricketsHP:0040281 - Very frequent48
HP:0002653HP:0002653Bone pain0EHHADH CL E G H19623247ORPHA:3337Primary Fanconi renotubular syndromeHP:0040282 - Frequent2
HP:0002653HP:0002653Bone pain0ELANE CL E G H19913309ORPHA:2686Cyclic neutropeniaHP:0040281 - Very frequent79
HP:0002653HP:0002653Bone pain0ENPP1 CL E G H51673356ORPHA:289176Autosomal recessive hypophosphatemic ricketsHP:0040281 - Very frequent151
HP:0002653HP:0002653Bone pain0EXT1 CL E G H21313512ORPHA:502Trichorhinophalangeal syndrome type 2HP:0040281 - Very frequent96
HP:0002653HP:0002653Bone pain0FGF23 CL E G H80743680ORPHA:89937Autosomal dominant hypophosphatemic ricketsHP:0040282 - Frequent51
HP:0002653HP:0002653Bone pain0FGF23 CL E G H80743680OMIM:193100Hypophosphatemic rickets, autosomal dominant.51
HP:0002653HP:0002653Bone pain0FIP1L1 CL E G H8160819124ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional4
HP:0002653HP:0002653Bone pain0FOXE1 CL E G H23043806ORPHA:319487Familial papillary or follicular thyroid carcinomaHP:0040283 - Occasional9
HP:0002653HP:0002653Bone pain0GATM CL E G H26284175ORPHA:3337Primary Fanconi renotubular syndromeHP:0040282 - Frequent86
HP:0002653HP:0002653Bone pain0GBA1 CL E G H26294177ORPHA:77259Gaucher disease type 1HP:0040281 - Very frequent
HP:0002653HP:0002653Bone pain0GBA1 CL E G H26294177ORPHA:77261Gaucher disease type 3HP:0040281 - Very frequent
HP:0002653HP:0002653Bone pain0GBA1 CL E G H26294177OMIM:230800Gaucher disease, type I.
HP:0002653HP:0002653Bone pain0GNAS CL E G H27784392ORPHA:57782Mazabraud syndromeHP:0040283 - Occasional101
HP:0002653HP:0002653Bone pain0GNAS CL E G H27784392ORPHA:562McCune-Albright syndromeHP:0040283 - Occasional101
HP:0002653HP:0002653Bone pain0GNAS CL E G H27784392ORPHA:2762Progressive osseous heteroplasiaHP:0040281 - Very frequent101
HP:0002653HP:0002653Bone pain0HABP2 CL E G H30264798ORPHA:319487Familial papillary or follicular thyroid carcinomaHP:0040283 - Occasional58
HP:0002653HP:0002653Bone pain0HPGD CL E G H32485154ORPHA:2796PachydermoperiostosisHP:0040281 - Very frequent55
HP:0002653HP:0002653Bone pain0IDH1 CL E G H34175382ORPHA:163634Maffucci syndromeHP:0040282 - Frequent15
HP:0002653HP:0002653Bone pain0IDH1 CL E G H34175382ORPHA:296Ollier diseaseHP:0040282 - Frequent15
HP:0002653HP:0002653Bone pain0IDH2 CL E G H34185383ORPHA:163634Maffucci syndromeHP:0040282 - Frequent29
HP:0002653HP:0002653Bone pain0IDH2 CL E G H34185383ORPHA:296Ollier diseaseHP:0040282 - Frequent29
HP:0002653HP:0002653Bone pain0IRF2BP2 CL E G H35994821729ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional4
HP:0002653HP:0002653Bone pain0KIF1B CL E G H2309516636OMIM:256700Neuroblastoma, susceptibility to.202
HP:0002653HP:0002653Bone pain0KIT CL E G H38156342ORPHA:98849Systemic mastocytosis with associated hematologic neoplasmHP:0040283 - Occasional327
HP:0002653HP:0002653Bone pain0LEMD3 CL E G H2359228887ORPHA:1306Buschke-Ollendorff syndromeHP:0040281 - Very frequent68
HP:0002653HP:0002653Bone pain0LEMD3 CL E G H2359228887ORPHA:166119Isolated osteopoikilosis68
HP:0002653HP:0002653Bone pain0LPIN2 CL E G H966314450ORPHA:77297Majeed syndromeHP:0040281 - Very frequent186
HP:0002653HP:0002653Bone pain0LPIN2 CL E G H966314450OMIM:609628MAJEED SYNDROME; MJDS186
HP:0002653HP:0002653Bone pain0MINPP1 CL E G H95627102ORPHA:319487Familial papillary or follicular thyroid carcinomaHP:0040283 - Occasional3
HP:0002653HP:0002653Bone pain0NABP1 CL E G H6485926232ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional
HP:0002653HP:0002653Bone pain0NDUFAF6 CL E G H13768228625ORPHA:3337Primary Fanconi renotubular syndromeHP:0040282 - Frequent39
HP:0002653HP:0002653Bone pain0NOTCH2 CL E G H48537882ORPHA:955Hajdu-Cheney syndromeHP:0040282 - Frequent138
HP:0002653HP:0002653Bone pain0NPM1 CL E G H48697910ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional12
HP:0002653HP:0002653Bone pain0NUMA1 CL E G H49268059ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional
HP:0002653HP:0002653Bone pain0PHEX CL E G H52518918OMIM:307800Hypophosphatemic rickets, X-linked dominant.217
HP:0002653HP:0002653Bone pain0PHEX CL E G H52518918ORPHA:89936X-linked hypophosphatemiaHP:0040282 - Frequent217
HP:0002653HP:0002653Bone pain0PML CL E G H53719113ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional3
HP:0002653HP:0002653Bone pain0POLE CL E G H54269177OMIM:615139Facial dysmorphism, immunodeficiency, livedo, and short statureHP:0040283 - Occasional1129
HP:0002653HP:0002653Bone pain0PRKAR1A CL E G H55739388ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional134
HP:0002653HP:0002653Bone pain0PSAP CL E G H56609498OMIM:610539Gaucher disease, atypical81
HP:0002653HP:0002653Bone pain0PSMB8 CL E G H56969545OMIM:256040Proteasome-associated autoinflammatory syndrome 1 and digenic forms20
HP:0002653HP:0002653Bone pain0PTH1R CL E G H57459608ORPHA:296Ollier diseaseHP:0040282 - Frequent58
HP:0002653HP:0002653Bone pain0PTPN11 CL E G H57819644ORPHA:2499MetachondromatosisHP:0040281 - Very frequent291
HP:0002653HP:0002653Bone pain0RARA CL E G H59149864ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional2
HP:0002653HP:0002653Bone pain0RUNX1 CL E G H86110471ORPHA:98850Aggressive systemic mastocytosisHP:0040282 - Frequent181
HP:0002653HP:0002653Bone pain0SCARB2 CL E G H9501665ORPHA:77259Gaucher disease type 1HP:0040281 - Very frequent77
HP:0002653HP:0002653Bone pain0SERPINF2 CL E G H53459075ORPHA:79Congenital alpha2-antiplasmin deficiencyHP:0040283 - Occasional8
HP:0002653HP:0002653Bone pain0SLC34A1 CL E G H656911019ORPHA:157215Hereditary hypophosphatemic rickets with hypercalciuriaHP:0040282 - Frequent47
HP:0002653HP:0002653Bone pain0SLC34A1 CL E G H656911019ORPHA:3337Primary Fanconi renotubular syndromeHP:0040282 - Frequent47
HP:0002653HP:0002653Bone pain0SLC34A3 CL E G H14268020305ORPHA:157215Hereditary hypophosphatemic rickets with hypercalciuriaHP:0040282 - Frequent52
HP:0002653HP:0002653Bone pain0SLC34A3 CL E G H14268020305OMIM:241530Hypophosphatemic rickets with hypercalciuria, hereditary.52
HP:0002653HP:0002653Bone pain0SLCO2A1 CL E G H657810955ORPHA:2796PachydermoperiostosisHP:0040281 - Very frequent13
HP:0002653HP:0002653Bone pain0SNX10 CL E G H2988714974ORPHA:667Autosomal recessive malignant osteopetrosisHP:0040281 - Very frequent2
HP:0002653HP:0002653Bone pain0SQSTM1 CL E G H887811280OMIM:167250Paget disease of bone 3.62
HP:0002653HP:0002653Bone pain0SRSF2 CL E G H642710783ORPHA:98850Aggressive systemic mastocytosisHP:0040282 - Frequent1
HP:0002653HP:0002653Bone pain0SRSF2 CL E G H642710783ORPHA:98849Systemic mastocytosis with associated hematologic neoplasmHP:0040283 - Occasional1
HP:0002653HP:0002653Bone pain0STAT3 CL E G H677411364ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional110
HP:0002653HP:0002653Bone pain0STAT5B CL E G H677711367ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional12
HP:0002653HP:0002653Bone pain0TBL1XR1 CL E G H7971829529ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional22
HP:0002653HP:0002653Bone pain0TCIRG1 CL E G H1031211647ORPHA:667Autosomal recessive malignant osteopetrosisHP:0040281 - Very frequent82
HP:0002653HP:0002653Bone pain0TEK CL E G H701011724ORPHA:1059Blue rubber bleb nevusHP:0040281 - Very frequent78
HP:0002653HP:0002653Bone pain0TET2 CL E G H5479025941ORPHA:98850Aggressive systemic mastocytosisHP:0040282 - Frequent3
HP:0002653HP:0002653Bone pain0TET2 CL E G H5479025941ORPHA:98849Systemic mastocytosis with associated hematologic neoplasmHP:0040283 - Occasional3
HP:0002653HP:0002653Bone pain0TGFB1 CL E G H704011766ORPHA:1328Camurati-Engelmann diseaseHP:0040281 - Very frequent13
HP:0002653HP:0002653Bone pain0TNFRSF11A CL E G H879211908OMIM:174810Familial expansile osteolysis.72
HP:0002653HP:0002653Bone pain0TNFRSF11A CL E G H879211908OMIM:602080Paget disease of bone 2, early-onset.72
HP:0002653HP:0002653Bone pain0TNFRSF1A CL E G H713211916OMIM:142680Periodic fever, familial, autosomal dominant131
HP:0002653HP:0002653Bone pain0TNFSF11 CL E G H860011926ORPHA:667Autosomal recessive malignant osteopetrosisHP:0040281 - Very frequent44
HP:0002653HP:0002653Bone pain0TREM2 CL E G H5420917761ORPHA:2770Nasu-Hakola diseaseHP:0040281 - Very frequent31
HP:0002653HP:0002653Bone pain0TRPS1 CL E G H722712340ORPHA:502Trichorhinophalangeal syndrome type 2HP:0040281 - Very frequent171
HP:0002653HP:0002653Bone pain0TYROBP CL E G H730512449ORPHA:2770Nasu-Hakola diseaseHP:0040281 - Very frequent22
HP:0002653HP:0002653Bone pain0VCP CL E G H741512666ORPHA:329475Spastic paraplegia-Paget disease of bone syndromeHP:0040281 - Very frequent63
HP:0002653HP:0002653Bone pain0VDR CL E G H742112679ORPHA:93160Hypocalcemic vitamin D-resistant ricketsHP:0040281 - Very frequent104
HP:0002653HP:0002653Bone pain0VDR CL E G H742112679OMIM:277440Vitamin d-dependent rickets, type 2A.104
HP:0002653HP:0002653Bone pain0WNT1 CL E G H747112774ORPHA:85193Idiopathic juvenile osteoporosisHP:0040281 - Very frequent12
HP:0002653HP:0002653Bone pain0WNT3A CL E G H8978015983ORPHA:85193Idiopathic juvenile osteoporosisHP:0040281 - Very frequent
HP:0002653HP:0002653Bone pain0ZBTB16 CL E G H770412930ORPHA:520Acute promyelocytic leukemiaHP:0040283 - Occasional1
HP:0002653HP:0002653Bone pain0ZNF687 CL E G H5759229277OMIM:616833Paget disease of bone 6.2


Genes (77) :AGXT AP2S1 ASXL1 ATP7B BCOR CBL CCND1 CDC73 CLCN5 CLCN7 CYP19A1 CYP27B1 CYP2R1 DKK1 DMP1 EHHADH ELANE ENPP1 EXT1 FGF23 FIP1L1 FOXE1 GATM GBA1 GNAS HABP2 HPGD IDH1 IDH2 IRF2BP2 KIF1B KIT LEMD3 LPIN2 MINPP1 NABP1 NDUFAF6 NOTCH2 NPM1 NUMA1 PHEX PML POLE PRKAR1A PSAP PSMB8 PTH1R PTPN11 RARA RUNX1 SCARB2 SERPINF2 SLC34A1 SLC34A3 SLCO2A1 SNX10 SQSTM1 SRSF2 STAT3 STAT5B TBL1XR1 TCIRG1 TEK TET2 TGFB1 TNFRSF11A TNFRSF1A TNFSF11 TREM2 TRPS1 TYROBP VCP VDR WNT1 WNT3A ZBTB16 ZNF687

Diseases (60) :OMIM:259900 OMIM:600740 ORPHA:98850 ORPHA:98849 ORPHA:905 ORPHA:520 ORPHA:29073 ORPHA:99880 ORPHA:143 OMIM:300009 OMIM:300554 ORPHA:53 ORPHA:667 ORPHA:91 ORPHA:289157 OMIM:264700 OMIM:600081 ORPHA:85193 ORPHA:289176 ORPHA:3337 ORPHA:2686 ORPHA:502 ORPHA:89937 OMIM:193100 ORPHA:319487 ORPHA:77259 ORPHA:77261 OMIM:230800 ORPHA:57782 ORPHA:562 ORPHA:2762 ORPHA:2796 ORPHA:163634 ORPHA:296 OMIM:256700 ORPHA:1306 ORPHA:166119 ORPHA:77297 OMIM:609628 ORPHA:955 OMIM:307800 ORPHA:89936 OMIM:615139 OMIM:610539 OMIM:256040 ORPHA:2499 ORPHA:79 ORPHA:157215 OMIM:241530 OMIM:167250 ORPHA:1059 ORPHA:1328 OMIM:174810 OMIM:602080 OMIM:142680 ORPHA:2770 ORPHA:329475 ORPHA:93160 OMIM:277440 OMIM:616833
 

Human Phenotype Ontology(HPO) is developed by the Human Phenotype Ontology Consortium. The version used here is December 15 2022 release.