Human Phenotype Ontology

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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:
Hematological neoplasm (HP:0004377)

Parent Node:
Lymphoma (HP:0002665)

..Starting node
..Non-Hodgkin lymphoma (HP:0012539)

Term ID:

12539

Name:

Non-Hodgkin lymphoma

Synonym:

Definition:

A type of lymphoma characterized microscopically by the absence of multinucleated Reed-Sternberg cells.

Comments:

Reference:

HP:0012539

Genes and Diseases:

Child Nodes:

........

T-cell lymphoma (HP:0012190)

................... HP:0005517 T-cell lymphoma/leukemia
................... HP:0012192 Cutaneous T-cell lymphoma
................... HP:0012193 Anaplastic large-cell lymphoma

........

B-cell lymphoma (HP:0012191)

........

Primary central nervous system lymphoma (HP:0030069)

........

Burkitt lymphoma (HP:0030080)

Sister Nodes:

Gastric lymphoma (HP:0045038)

Hodgkin lymphoma (HP:0012189)

Pulmonary lymphoma (HP:0011953)

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:0012539	HP:0012539	Non-Hodgkin lymphoma	0	ADA CL E G H	100	186	OMIM:102700	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency		75
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	ATM CL E G H	472	795	OMIM:208900	ATAXIA-TELANGIECTASIA	.	3267
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	ATM CL E G H	472	795	ORPHA:52416	Mantle cell lymphoma		3267
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	BCL10 CL E G H	8915	989	ORPHA:52417	MALT lymphoma		18
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	BIRC3 CL E G H	330	591	ORPHA:52417	MALT lymphoma
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CASP10 CL E G H	843	1500	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	87
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CCND1 CL E G H	595	1582	ORPHA:52416	Mantle cell lymphoma		1
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CD28 CL E G H	940	1653	ORPHA:2584	Classic mycosis fungoides
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CD28 CL E G H	940	1653	ORPHA:3162	Sézary syndrome
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CDKN2A CL E G H	1029	1787	ORPHA:524	Li-Fraumeni syndrome	HP:0040284 - Very rare	289
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CHEK2 CL E G H	11200	16627	ORPHA:524	Li-Fraumeni syndrome	HP:0040284 - Very rare	833
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CTLA4 CL E G H	1493	2505	ORPHA:2584	Classic mycosis fungoides		10
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	CTLA4 CL E G H	1493	2505	ORPHA:3162	Sézary syndrome		10
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	FAS CL E G H	355	11920	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	59
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	FASLG CL E G H	356	11936	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	37
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	FCHO1 CL E G H	23149	29002	OMIM:619164	IMMUNODEFICIENCY 76; IMD76
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	FOXP1 CL E G H	27086	3823	ORPHA:52417	MALT lymphoma		184
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	IGH CL E G H	3492	5477	ORPHA:52417	MALT lymphoma		7
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	IGH CL E G H	3492	5477	ORPHA:52416	Mantle cell lymphoma		7
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	IKZF3 CL E G H	22806	13178	OMIM:619437	IMMUNODEFICIENCY 84; IMD84
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	ITK CL E G H	3702	6171	OMIM:613011	LYMPHOPROLIFERATIVE SYNDROME 1; LPFS1		51
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MAGT1 CL E G H	84061	28880	OMIM:300853	IMMUNODEFICIENCY, X-LINKED, WITH MAGNESIUM DEFECT, EPSTEIN-BARR VIRUS INFECTION, AND NEOPLASIA; XMEN		17
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MALT1 CL E G H	10892	6819	ORPHA:52417	MALT lymphoma		6
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MDM2 CL E G H	4193	6973	ORPHA:524	Li-Fraumeni syndrome	HP:0040284 - Very rare	1
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MLH1 CL E G H	4292	7127	OMIM:276300	Mismatch repair cancer syndrome 1		1819
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MSH6 CL E G H	2956	7329	OMIM:619097	MISMATCH REPAIR CANCER SYNDROME 3; MMRCS3		2232
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	MYC CL E G H	4609	7553	OMIM:113970	Burkitt lymphoma		11
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	NBN CL E G H	4683	7652	ORPHA:647	Nijmegen breakage syndrome		706
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	NTHL1 CL E G H	4913	8028	ORPHA:454840	NTHL1-related attenuated familial adenomatous polyposis	HP:0040283 - Occasional	2
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	PIK3R1 CL E G H	5295	8979	OMIM:616005	Immunodeficiency 36		43
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	PMS2 CL E G H	5395	9122	OMIM:619101	MISMATCH REPAIR CANCER SYNDROME 4; MMRCS4		1121
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	POLE CL E G H	5426	9177	OMIM:618336	Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency		1129
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	PRKCD CL E G H	5580	9399	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	10
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	PTPRC CL E G H	5788	9666	OMIM:619924			25
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	RASGRP1 CL E G H	10125	9878	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	RASGRP1 CL E G H	10125	9878	OMIM:618534	IMMUNODEFICIENCY 64; IMD64
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	RHOH CL E G H	399	686	OMIM:618307	Epidermodysplasia verruciformis, susceptibility to, 4
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	SH2D1A CL E G H	4068	10820	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		37
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	SMARCAL1 CL E G H	50485	11102	ORPHA:1830	Schimke immuno-osseous dysplasia	HP:0040284 - Very rare	74
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	SYK CL E G H	6850	11491	OMIM:619381	IMMUNODEFICIENCY 82 WITH SYSTEMIC INFLAMMATION; IMD82		1
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	TNFRSF1B CL E G H	7133	11917	ORPHA:2584	Classic mycosis fungoides
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	TNFRSF1B CL E G H	7133	11917	ORPHA:3162	Sézary syndrome
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	TP53 CL E G H	7157	11998	ORPHA:524	Li-Fraumeni syndrome	HP:0040284 - Very rare	911
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	TTC7A CL E G H	57217	19750	OMIM:243150	Gastrointestinal defects and immunodeficiency syndrome		26
HP:0012539	HP:0012539	Non-Hodgkin lymphoma	0	XIAP CL E G H	331	592	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		81
HP:0012539	HP:0030069	Primary central nervous system lymphoma	1	CL E G H
HP:0012539	HP:0012191	B-cell lymphoma	1	ADA CL E G H	100	186	OMIM:102700	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency	.	75
HP:0012539	HP:0012191	B-cell lymphoma	1	ATM CL E G H	472	795	ORPHA:52416	Mantle cell lymphoma	HP:0040281 - Very frequent	3267
HP:0012539	HP:0012191	B-cell lymphoma	1	BCL10 CL E G H	8915	989	ORPHA:52417	MALT lymphoma	HP:0040281 - Very frequent	18
HP:0012539	HP:0012191	B-cell lymphoma	1	BIRC3 CL E G H	330	591	ORPHA:52417	MALT lymphoma	HP:0040281 - Very frequent
HP:0012539	HP:0012191	B-cell lymphoma	1	CASP10 CL E G H	843	1500	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	87
HP:0012539	HP:0012190	T-cell lymphoma	1	CASP10 CL E G H	843	1500	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	87
HP:0012539	HP:0030080	Burkitt lymphoma	1	CASP10 CL E G H	843	1500	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	87
HP:0012539	HP:0012191	B-cell lymphoma	1	CCND1 CL E G H	595	1582	ORPHA:52416	Mantle cell lymphoma	HP:0040281 - Very frequent	1
HP:0012539	HP:0012190	T-cell lymphoma	1	CD28 CL E G H	940	1653	ORPHA:2584	Classic mycosis fungoides
HP:0012539	HP:0012190	T-cell lymphoma	1	CD28 CL E G H	940	1653	ORPHA:3162	Sézary syndrome
HP:0012539	HP:0012190	T-cell lymphoma	1	CTLA4 CL E G H	1493	2505	ORPHA:2584	Classic mycosis fungoides		10
HP:0012539	HP:0012190	T-cell lymphoma	1	CTLA4 CL E G H	1493	2505	ORPHA:3162	Sézary syndrome		10
HP:0012539	HP:0012191	B-cell lymphoma	1	FAS CL E G H	355	11920	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	59
HP:0012539	HP:0030080	Burkitt lymphoma	1	FAS CL E G H	355	11920	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	59
HP:0012539	HP:0012190	T-cell lymphoma	1	FAS CL E G H	355	11920	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	59
HP:0012539	HP:0012191	B-cell lymphoma	1	FASLG CL E G H	356	11936	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	37
HP:0012539	HP:0012190	T-cell lymphoma	1	FASLG CL E G H	356	11936	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	37
HP:0012539	HP:0030080	Burkitt lymphoma	1	FASLG CL E G H	356	11936	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	37
HP:0012539	HP:0012191	B-cell lymphoma	1	FCHO1 CL E G H	23149	29002	OMIM:619164	IMMUNODEFICIENCY 76; IMD76
HP:0012539	HP:0012191	B-cell lymphoma	1	FOXP1 CL E G H	27086	3823	ORPHA:52417	MALT lymphoma	HP:0040281 - Very frequent	184
HP:0012539	HP:0012191	B-cell lymphoma	1	IGH CL E G H	3492	5477	ORPHA:52417	MALT lymphoma	HP:0040281 - Very frequent	7
HP:0012539	HP:0012191	B-cell lymphoma	1	IGH CL E G H	3492	5477	ORPHA:52416	Mantle cell lymphoma	HP:0040281 - Very frequent	7
HP:0012539	HP:0012191	B-cell lymphoma	1	IKZF3 CL E G H	22806	13178	OMIM:619437	IMMUNODEFICIENCY 84; IMD84
HP:0012539	HP:0012191	B-cell lymphoma	1	ITK CL E G H	3702	6171	OMIM:613011	LYMPHOPROLIFERATIVE SYNDROME 1; LPFS1		51
HP:0012539	HP:0012191	B-cell lymphoma	1	MAGT1 CL E G H	84061	28880	OMIM:300853	IMMUNODEFICIENCY, X-LINKED, WITH MAGNESIUM DEFECT, EPSTEIN-BARR VIRUS INFECTION, AND NEOPLASIA; XMEN		17
HP:0012539	HP:0012191	B-cell lymphoma	1	MALT1 CL E G H	10892	6819	ORPHA:52417	MALT lymphoma	HP:0040281 - Very frequent	6
HP:0012539	HP:0012190	T-cell lymphoma	1	MLH1 CL E G H	4292	7127	OMIM:276300	Mismatch repair cancer syndrome 1		1819
HP:0012539	HP:0012190	T-cell lymphoma	1	MSH6 CL E G H	2956	7329	OMIM:619097	MISMATCH REPAIR CANCER SYNDROME 3; MMRCS3		2232
HP:0012539	HP:0030080	Burkitt lymphoma	1	MYC CL E G H	4609	7553	OMIM:113970	Burkitt lymphoma	.	11
HP:0012539	HP:0012190	T-cell lymphoma	1	NBN CL E G H	4683	7652	ORPHA:647	Nijmegen breakage syndrome	HP:0040283 - Occasional	706
HP:0012539	HP:0012191	B-cell lymphoma	1	NBN CL E G H	4683	7652	ORPHA:647	Nijmegen breakage syndrome	HP:0040283 - Occasional	706
HP:0012539	HP:0012191	B-cell lymphoma	1	PIK3R1 CL E G H	5295	8979	OMIM:616005	Immunodeficiency 36	HP:0040284 - Very rare	43
HP:0012539	HP:0012190	T-cell lymphoma	1	POLE CL E G H	5426	9177	OMIM:618336	Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency	HP:0040284 - Very rare	1129
HP:0012539	HP:0012190	T-cell lymphoma	1	PRKCD CL E G H	5580	9399	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	10
HP:0012539	HP:0030080	Burkitt lymphoma	1	PRKCD CL E G H	5580	9399	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	10
HP:0012539	HP:0012191	B-cell lymphoma	1	PRKCD CL E G H	5580	9399	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional	10
HP:0012539	HP:0012191	B-cell lymphoma	1	PTPRC CL E G H	5788	9666	OMIM:619924			25
HP:0012539	HP:0030080	Burkitt lymphoma	1	RASGRP1 CL E G H	10125	9878	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional
HP:0012539	HP:0012191	B-cell lymphoma	1	RASGRP1 CL E G H	10125	9878	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional
HP:0012539	HP:0012190	T-cell lymphoma	1	RASGRP1 CL E G H	10125	9878	ORPHA:3261	Autoimmune lymphoproliferative syndrome	HP:0040283 - Occasional
HP:0012539	HP:0012191	B-cell lymphoma	1	RASGRP1 CL E G H	10125	9878	OMIM:618534	IMMUNODEFICIENCY 64; IMD64
HP:0012539	HP:0030080	Burkitt lymphoma	1	RHOH CL E G H	399	686	OMIM:618307	Epidermodysplasia verruciformis, susceptibility to, 4	.
HP:0012539	HP:0030080	Burkitt lymphoma	1	SH2D1A CL E G H	4068	10820	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		37
HP:0012539	HP:0012191	B-cell lymphoma	1	SYK CL E G H	6850	11491	OMIM:619381	IMMUNODEFICIENCY 82 WITH SYSTEMIC INFLAMMATION; IMD82		1
HP:0012539	HP:0012190	T-cell lymphoma	1	TNFRSF1B CL E G H	7133	11917	ORPHA:2584	Classic mycosis fungoides
HP:0012539	HP:0012190	T-cell lymphoma	1	TNFRSF1B CL E G H	7133	11917	ORPHA:3162	Sézary syndrome
HP:0012539	HP:0012190	T-cell lymphoma	1	TTC7A CL E G H	57217	19750	OMIM:243150	Gastrointestinal defects and immunodeficiency syndrome		26
HP:0012539	HP:0030080	Burkitt lymphoma	1	XIAP CL E G H	331	592	OMIM:308240	Lymphoproliferative syndrome, X-linked, 1		81
HP:0012539	HP:0012193	Anaplastic large-cell lymphoma	2	CL E G H
HP:0012539	HP:0005517	T-cell lymphoma/leukemia	2	CL E G H
HP:0012539	HP:0034403	Subcutaneous panniculitis-like T-cell lymphoma	2	CL E G H
HP:0012539	HP:0033125	Follicular lymphoma	2	CL E G H
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	CD28 CL E G H	940	1653	ORPHA:2584	Classic mycosis fungoides	HP:0040282 - Frequent
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	CD28 CL E G H	940	1653	ORPHA:3162	Sézary syndrome	HP:0040281 - Very frequent
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	CTLA4 CL E G H	1493	2505	ORPHA:2584	Classic mycosis fungoides	HP:0040282 - Frequent	10
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	CTLA4 CL E G H	1493	2505	ORPHA:3162	Sézary syndrome	HP:0040281 - Very frequent	10
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	TNFRSF1B CL E G H	7133	11917	ORPHA:2584	Classic mycosis fungoides	HP:0040282 - Frequent
HP:0012539	HP:0012192	Cutaneous T-cell lymphoma	2	TNFRSF1B CL E G H	7133	11917	ORPHA:3162	Sézary syndrome	HP:0040281 - Very frequent

Genes (39) :ADA ATM BCL10 BIRC3 CASP10 CCND1 CD28 CDKN2A CHEK2 CTLA4 FAS FASLG FCHO1 FOXP1 IGH IKZF3 ITK MAGT1 MALT1 MDM2 MLH1 MSH6 MYC NBN NTHL1 PIK3R1 PMS2 POLE PRKCD PTPRC RASGRP1 RHOH SH2D1A SMARCAL1 SYK TNFRSF1B TP53 TTC7A XIAP

Diseases (27) :OMIM:102700 OMIM:208900 ORPHA:52416 ORPHA:52417 ORPHA:3261 ORPHA:2584 ORPHA:3162 ORPHA:524 OMIM:619164 OMIM:619437 OMIM:613011 OMIM:300853 OMIM:276300 OMIM:619097 OMIM:113970 ORPHA:647 ORPHA:454840 OMIM:616005 OMIM:619101 OMIM:618336 OMIM:619924 OMIM:618534 OMIM:618307 OMIM:308240 ORPHA:1830 OMIM:619381 OMIM:243150

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

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