Human Phenotype Ontology

About
MSeqDR-LSDB
Tools
- Quick-Mitome for WES
- Quick-Mitome
- Quick-Mitome Report
- mtDNA Tool:
- mvTool
- Phy-Mer
- MToolBox
- mvTool for Haplogroup
- mvTool with HmtDB
- MitoMaster
- MitoTIP tRNA Scoring
- MSeq-OpenCGA
- Variant Tool:
- VariantOneStop
- HBCR Exome (Retired)
- POLG Patho. Server
- Data - Awsomics GeEx
- Expert Panel
- Panel Tool:
- Gene Panel Examiner
- Transgenomic_NuclearMitome
- Pedigree Maker
- json2table
Phenome-Disease
Collaboration
- Genesis (GEM.App)
- LeighMap
- Expert Panel
- Collaboration Zone
Submission
- Submit_Interpret_Variant
- Instructions

Hello! Guest! Please Login or Register! Clinician Mode

Examples Gene: MT-ND1, POLG, Region: M:1-1000 Variant: m.8993T>G, 1:g.10042757T>C rs3888511 MSCV_0000006, ClinVar: RCV000000015, Disease: Leigh syndrome, Phenotype: Retinopathy

Grandparent Node:
Abnormal leukocyte morphology (HP:0001881)

Parent Node:
Abnormal myeloid leukocyte morphology (HP:0010974)

..Starting node
..Abnormal macrophage morphology (HP:0004311)

Term ID:

4311

Name:

Abnormal macrophage morphology

Synonym:

Abnormality of histiocytes; Abnormality of macrophages

Definition:

An abnormality of macrophages.

Comments:

Reference:

HP:0004311

Genes and Diseases:

Child Nodes:

........

Sea-blue histiocytosis (HP:0001982)

........

Granulomatosis (HP:0002955)

................... HP:0011955 Hepatic granulomatosis
................... HP:0012220 Non-caseating epithelioid cell granulomatosis
................... HP:0040139 Lipogranulomatosis
................... HP:0100313 Cerebral granulomatosis

........

Bone-marrow foam cells (HP:0004333)

........

Hemophagocytosis (HP:0012156)

........

Abnormal macrophage count (HP:0030326)

................... HP:0030327 Abnormal osteoclast count

........

Histiocytosis (HP:0100727)

................... HP:0040138 Mucinous histiocytosis

Sister Nodes:

Abnormal granulocyte morphology (HP:0001911)

Abnormal mast cell morphology (HP:0100494)

Abnormal phagocytosis (HP:0010977)

Input	HPO ID	HPO term	Distance	Gene	Gene id entrez	HGNC ID	DiseaseId	DiseaseName	Frequency	ClinVar variants
HPO disease - gene - phenotype typical associations:
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	APOE CL E G H	348	613	OMIM:269600	Sea-Blue histiocyte disease		39
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	APOE CL E G H	348	613	ORPHA:158029	Sea-blue histiocytosis		39
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	ASAH1 CL E G H	427	735	OMIM:228000	Farber lipogranulomatosis		78
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	CD27 CL E G H	939	11922	OMIM:615122	Lymphoproliferative syndrome 2		4
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	CTLA4 CL E G H	1493	2505	ORPHA:900	Granulomatosis with polyangiitis		10
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	CYBA CL E G H	1535	2577	OMIM:233690	GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, CYTOCHROME b-NEGATIVE		27
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	CYBB CL E G H	1536	2578	OMIM:306400	Chronic granulomatous disease, X-linked		111
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	DNASE2 CL E G H	1777	2960	OMIM:619858
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	GLB1 CL E G H	2720	4298	OMIM:230600	Gm1-gangliosidosis, type II		120
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	HAVCR2 CL E G H	84868	18437	ORPHA:86884	Subcutaneous panniculitis-like T-cell lymphoma
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	HAVCR2 CL E G H	84868	18437	OMIM:618398	T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	HLA-DPA1 CL E G H	3113	4938	ORPHA:900	Granulomatosis with polyangiitis
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	HLA-DPB1 CL E G H	3115	4940	ORPHA:900	Granulomatosis with polyangiitis		1
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	IFNGR1 CL E G H	3459	5439	OMIM:209950	Immunodeficiency 27A, mycobacteriosis, AR		60
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	LIPA CL E G H	3988	6617	OMIM:278000	Lysosomal acid lipase deficiency		73
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	LIPA CL E G H	3988	6617	ORPHA:75233	Wolman disease		73
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	LYST CL E G H	1130	1968	ORPHA:167	Chédiak-Higashi syndrome		239
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	LYST CL E G H	1130	1968	OMIM:214500	Chediak-Higashi syndrome		239
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	NCF1 CL E G H	653361	7660	OMIM:233700	Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type I		13
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	NCF2 CL E G H	4688	7661	OMIM:233710	Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type II		67
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	NEU1 CL E G H	4758	7758	OMIM:256550	Neuraminidase deficiency		43
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	NPC1 CL E G H	4864	7897	OMIM:257220	Niemann-pick disease, type C1		258
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	NPC2 CL E G H	10577	14537	OMIM:607625	Niemann-pick disease, type C2		33
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	PIK3CG CL E G H	5294	8978	OMIM:619802	IMMUNODEFICIENCY 97 WITH AUTOINFLAMMATION; IMD97		2
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	PRF1 CL E G H	5551	9360	ORPHA:540	Familial hemophagocytic lymphohistiocytosis		58
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	PRF1 CL E G H	5551	9360	OMIM:603553	Hemophagocytic lymphohistiocytosis, familial, 2		58
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	PRTN3 CL E G H	5657	9495	ORPHA:900	Granulomatosis with polyangiitis
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	PTPN22 CL E G H	26191	9652	ORPHA:900	Granulomatosis with polyangiitis		3
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	RAB27A CL E G H	5873	9766	ORPHA:79477	Griscelli syndrome type 2		67
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	RAB27A CL E G H	5873	9766	OMIM:607624	Griscelli syndrome, type 2		67
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SAMD9L CL E G H	219285	1349	ORPHA:2585	Ataxia-pancytopenia syndrome	HP:0040282 - Frequent	4
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SGCG CL E G H	6445	10809	ORPHA:353	Gamma-sarcoglycan-related limb-girdle muscular dystrophy R5	HP:0040282 - Frequent	83
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SH2D1A CL E G H	4068	10820	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		37
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SLC29A3 CL E G H	55315	23096	ORPHA:168569	H syndrome		68
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SLC29A3 CL E G H	55315	23096	OMIM:602782	Histiocytosis-lymphadenopathy plus syndrome		68
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SLC7A7 CL E G H	9056	11065	ORPHA:470	Lysinuric protein intolerance		104
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SLC7A7 CL E G H	9056	11065	OMIM:222700	Lysinuric protein intolerance		104
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SMPD1 CL E G H	6609	11120	OMIM:257200	Niemann-Pick disease, type A		164
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	SMPD1 CL E G H	6609	11120	OMIM:607616	Niemann-pick disease, type B		164
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	STX11 CL E G H	8676	11429	ORPHA:540	Familial hemophagocytic lymphohistiocytosis		85
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	STX11 CL E G H	8676	11429	OMIM:603552	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 4; FHL4		85
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	STXBP2 CL E G H	6813	11445	ORPHA:540	Familial hemophagocytic lymphohistiocytosis		70
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	STXBP2 CL E G H	6813	11445	OMIM:613101	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 5; FHL5		70
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	TLR8 CL E G H	51311	15632	OMIM:301078	IMMUNODEFICIENCY 98 WITH AUTOINFLAMMATION, X-LINKED; IMD98
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	UNC13D CL E G H	201294	23147	ORPHA:540	Familial hemophagocytic lymphohistiocytosis		116
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	UNC13D CL E G H	201294	23147	OMIM:608898	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 3; FHL3		116
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	XIAP CL E G H	331	592	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		81
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	XIAP CL E G H	331	592	OMIM:300635	Lymphoproliferative syndrome, X-linked, 2		81
HP:0004311	HP:0004311	Abnormal macrophage morphology	0	ZNFX1 CL E G H	57169	29271	OMIM:619644	IMMUNODEFICIENCY 91 AND HYPERINFLAMMATION; IMD91
HP:0004311	HP:0033046	Michaelis-Gutmann bodies	1	CL E G H
HP:0004311	HP:0030326	Abnormal macrophage count	1	CL E G H
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	APOE CL E G H	348	613	OMIM:269600	Sea-Blue histiocyte disease	.	39
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	APOE CL E G H	348	613	ORPHA:158029	Sea-blue histiocytosis	HP:0040281 - Very frequent	39
HP:0004311	HP:0002955	Granulomatosis	1	ASAH1 CL E G H	427	735	OMIM:228000	Farber lipogranulomatosis		78
HP:0004311	HP:0012156	Hemophagocytosis	1	CD27 CL E G H	939	11922	OMIM:615122	Lymphoproliferative syndrome 2		4
HP:0004311	HP:0002955	Granulomatosis	1	CTLA4 CL E G H	1493	2505	ORPHA:900	Granulomatosis with polyangiitis	HP:0040281 - Very frequent	10
HP:0004311	HP:0002955	Granulomatosis	1	CYBA CL E G H	1535	2577	OMIM:233690	GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, CYTOCHROME b-NEGATIVE	.	27
HP:0004311	HP:0002955	Granulomatosis	1	CYBB CL E G H	1536	2578	OMIM:306400	Chronic granulomatous disease, X-linked	.	111
HP:0004311	HP:0012156	Hemophagocytosis	1	DNASE2 CL E G H	1777	2960	OMIM:619858
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	GLB1 CL E G H	2720	4298	OMIM:230600	Gm1-gangliosidosis, type II	.	120
HP:0004311	HP:0012156	Hemophagocytosis	1	HAVCR2 CL E G H	84868	18437	ORPHA:86884	Subcutaneous panniculitis-like T-cell lymphoma	HP:0040282 - Frequent
HP:0004311	HP:0012156	Hemophagocytosis	1	HAVCR2 CL E G H	84868	18437	OMIM:618398	T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE	HP:0040284 - Very rare
HP:0004311	HP:0002955	Granulomatosis	1	HLA-DPA1 CL E G H	3113	4938	ORPHA:900	Granulomatosis with polyangiitis	HP:0040281 - Very frequent
HP:0004311	HP:0002955	Granulomatosis	1	HLA-DPB1 CL E G H	3115	4940	ORPHA:900	Granulomatosis with polyangiitis	HP:0040281 - Very frequent	1
HP:0004311	HP:0100727	Histiocytosis	1	IFNGR1 CL E G H	3459	5439	OMIM:209950	Immunodeficiency 27A, mycobacteriosis, AR		60
HP:0004311	HP:0004333	Bone-marrow foam cells	1	LIPA CL E G H	3988	6617	OMIM:278000	Lysosomal acid lipase deficiency	.	73
HP:0004311	HP:0004333	Bone-marrow foam cells	1	LIPA CL E G H	3988	6617	ORPHA:75233	Wolman disease	HP:0040283 - Occasional	73
HP:0004311	HP:0012156	Hemophagocytosis	1	LYST CL E G H	1130	1968	ORPHA:167	Chédiak-Higashi syndrome	HP:0040281 - Very frequent	239
HP:0004311	HP:0012156	Hemophagocytosis	1	LYST CL E G H	1130	1968	OMIM:214500	Chediak-Higashi syndrome		239
HP:0004311	HP:0002955	Granulomatosis	1	NCF1 CL E G H	653361	7660	OMIM:233700	Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type I	.	13
HP:0004311	HP:0002955	Granulomatosis	1	NCF2 CL E G H	4688	7661	OMIM:233710	Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type II	.	67
HP:0004311	HP:0004333	Bone-marrow foam cells	1	NEU1 CL E G H	4758	7758	OMIM:256550	Neuraminidase deficiency	.	43
HP:0004311	HP:0004333	Bone-marrow foam cells	1	NPC1 CL E G H	4864	7897	OMIM:257220	Niemann-pick disease, type C1	.	258
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	NPC1 CL E G H	4864	7897	OMIM:257220	Niemann-pick disease, type C1		258
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	NPC2 CL E G H	10577	14537	OMIM:607625	Niemann-pick disease, type C2	.	33
HP:0004311	HP:0004333	Bone-marrow foam cells	1	NPC2 CL E G H	10577	14537	OMIM:607625	Niemann-pick disease, type C2	.	33
HP:0004311	HP:0012156	Hemophagocytosis	1	PIK3CG CL E G H	5294	8978	OMIM:619802	IMMUNODEFICIENCY 97 WITH AUTOINFLAMMATION; IMD97		2
HP:0004311	HP:0012156	Hemophagocytosis	1	PRF1 CL E G H	5551	9360	ORPHA:540	Familial hemophagocytic lymphohistiocytosis	HP:0040281 - Very frequent	58
HP:0004311	HP:0012156	Hemophagocytosis	1	PRF1 CL E G H	5551	9360	OMIM:603553	Hemophagocytic lymphohistiocytosis, familial, 2		58
HP:0004311	HP:0002955	Granulomatosis	1	PRTN3 CL E G H	5657	9495	ORPHA:900	Granulomatosis with polyangiitis	HP:0040281 - Very frequent
HP:0004311	HP:0002955	Granulomatosis	1	PTPN22 CL E G H	26191	9652	ORPHA:900	Granulomatosis with polyangiitis	HP:0040281 - Very frequent	3
HP:0004311	HP:0012156	Hemophagocytosis	1	RAB27A CL E G H	5873	9766	ORPHA:79477	Griscelli syndrome type 2	HP:0040281 - Very frequent	67
HP:0004311	HP:0012156	Hemophagocytosis	1	RAB27A CL E G H	5873	9766	OMIM:607624	Griscelli syndrome, type 2		67
HP:0004311	HP:0012156	Hemophagocytosis	1	SH2D1A CL E G H	4068	10820	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		37
HP:0004311	HP:0100727	Histiocytosis	1	SLC29A3 CL E G H	55315	23096	ORPHA:168569	H syndrome	HP:0040281 - Very frequent	68
HP:0004311	HP:0100727	Histiocytosis	1	SLC29A3 CL E G H	55315	23096	OMIM:602782	Histiocytosis-lymphadenopathy plus syndrome		68
HP:0004311	HP:0012156	Hemophagocytosis	1	SLC7A7 CL E G H	9056	11065	ORPHA:470	Lysinuric protein intolerance	HP:0040282 - Frequent	104
HP:0004311	HP:0012156	Hemophagocytosis	1	SLC7A7 CL E G H	9056	11065	OMIM:222700	Lysinuric protein intolerance	.	104
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	SMPD1 CL E G H	6609	11120	OMIM:257200	Niemann-Pick disease, type A	.	164
HP:0004311	HP:0004333	Bone-marrow foam cells	1	SMPD1 CL E G H	6609	11120	OMIM:257200	Niemann-Pick disease, type A	.	164
HP:0004311	HP:0001982	Sea-blue histiocytosis	1	SMPD1 CL E G H	6609	11120	OMIM:607616	Niemann-pick disease, type B	.	164
HP:0004311	HP:0004333	Bone-marrow foam cells	1	SMPD1 CL E G H	6609	11120	OMIM:607616	Niemann-pick disease, type B	.	164
HP:0004311	HP:0012156	Hemophagocytosis	1	STX11 CL E G H	8676	11429	ORPHA:540	Familial hemophagocytic lymphohistiocytosis	HP:0040281 - Very frequent	85
HP:0004311	HP:0012156	Hemophagocytosis	1	STX11 CL E G H	8676	11429	OMIM:603552	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 4; FHL4		85
HP:0004311	HP:0012156	Hemophagocytosis	1	STXBP2 CL E G H	6813	11445	ORPHA:540	Familial hemophagocytic lymphohistiocytosis	HP:0040281 - Very frequent	70
HP:0004311	HP:0012156	Hemophagocytosis	1	STXBP2 CL E G H	6813	11445	OMIM:613101	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 5; FHL5		70
HP:0004311	HP:0012156	Hemophagocytosis	1	TLR8 CL E G H	51311	15632	OMIM:301078	IMMUNODEFICIENCY 98 WITH AUTOINFLAMMATION, X-LINKED; IMD98
HP:0004311	HP:0012156	Hemophagocytosis	1	UNC13D CL E G H	201294	23147	ORPHA:540	Familial hemophagocytic lymphohistiocytosis	HP:0040281 - Very frequent	116
HP:0004311	HP:0012156	Hemophagocytosis	1	UNC13D CL E G H	201294	23147	OMIM:608898	HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 3; FHL3		116
HP:0004311	HP:0012156	Hemophagocytosis	1	XIAP CL E G H	331	592	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		81
HP:0004311	HP:0012156	Hemophagocytosis	1	XIAP CL E G H	331	592	OMIM:300635	Lymphoproliferative syndrome, X-linked, 2		81
HP:0004311	HP:0012156	Hemophagocytosis	1	ZNFX1 CL E G H	57169	29271	OMIM:619644	IMMUNODEFICIENCY 91 AND HYPERINFLAMMATION; IMD91
HP:0004311	HP:0100313	Cerebral granulomatosis	2	CL E G H
HP:0004311	HP:0040138	Mucinous histiocytosis	2	CL E G H
HP:0004311	HP:0012220	Non-caseating epithelioid cell granulomatosis	2	CL E G H
HP:0004311	HP:0011955	Hepatic granulomatosis	2	CL E G H
HP:0004311	HP:0040139	Lipogranulomatosis	2	ASAH1 CL E G H	427	735	OMIM:228000	Farber lipogranulomatosis	.	78

Genes (36) :APOE ASAH1 CD27 CTLA4 CYBA CYBB DNASE2 GLB1 HAVCR2 HLA-DPA1 HLA-DPB1 IFNGR1 LIPA LYST NCF1 NCF2 NEU1 NPC1 NPC2 PIK3CG PRF1 PRTN3 PTPN22 RAB27A SAMD9L SGCG SH2D1A SLC29A3 SLC7A7 SMPD1 STX11 STXBP2 TLR8 UNC13D XIAP ZNFX1

Diseases (41) :OMIM:269600 ORPHA:158029 OMIM:228000 OMIM:615122 ORPHA:900 OMIM:233690 OMIM:306400 OMIM:619858 OMIM:230600 ORPHA:86884 OMIM:618398 OMIM:209950 OMIM:278000 ORPHA:75233 ORPHA:167 OMIM:214500 OMIM:233700 OMIM:233710 OMIM:256550 OMIM:257220 OMIM:607625 OMIM:619802 ORPHA:540 OMIM:603553 ORPHA:79477 OMIM:607624 ORPHA:2585 ORPHA:353 OMIM:308240 ORPHA:168569 OMIM:602782 ORPHA:470 OMIM:222700 OMIM:257200 OMIM:607616 OMIM:603552 OMIM:613101 OMIM:301078 OMIM:608898 OMIM:300635 OMIM:619644

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

Feedback about the webpages , or email to MSeqDR webmaster: Lishuang Shen