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:
Abnormal lymphocyte morphology (HP:0004332)

Grandparent Node:
Leukopenia (HP:0001882)

Parent Node:
Lymphopenia (HP:0001888)

..Starting node
..B lymphocytopenia (HP:0010976)

Term ID:

10976

Name:

B lymphocytopenia

Synonym:

B cell deficiency; B cell lymphopenia; Decreased B cell count; Low B cell count; Reduction in B cell number

Definition:

An abnormal decrease from the normal count of B cells.

Comments:

Reference:

HP:0010976

Genes and Diseases:

Child Nodes:

........

Severe B lymphocytopenia (HP:0005365)

........

Absence of mature B cells (HP:0030252)

................... HP:0030251 Absence of memory B cells

Sister Nodes:

T lymphocytopenia (HP:0005403)

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:0010976	HP:0010976	B lymphocytopenia	0	ADA CL E G H	100	186	ORPHA:277	Severe combined immunodeficiency due to adenosine deaminase deficiency	HP:0040282 - Frequent	75
HP:0010976	HP:0010976	B lymphocytopenia	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:0010976	HP:0010976	B lymphocytopenia	0	ALG12 CL E G H	79087	19358	ORPHA:79324	ALG12-CDG	HP:0040282 - Frequent	68
HP:0010976	HP:0010976	B lymphocytopenia	0	ARHGEF1 CL E G H	9138	681	OMIM:618459	Immunodeficiency 62
HP:0010976	HP:0010976	B lymphocytopenia	0	ATP11A CL E G H	23250	13552	OMIM:619851	LEUKODYSTROPHY, HYPOMYELINATING, 24; HLD24
HP:0010976	HP:0010976	B lymphocytopenia	0	B2M CL E G H	567	914	OMIM:241600	Immunodeficiency 43		8
HP:0010976	HP:0010976	B lymphocytopenia	0	BTK CL E G H	695	1133	OMIM:300755	Agammaglobulinemia, X-linked		109
HP:0010976	HP:0010976	B lymphocytopenia	0	BTK CL E G H	695	1133	OMIM:307200	Isolated growth hormone deficiency, type III, with agammaglobulinemia		109
HP:0010976	HP:0010976	B lymphocytopenia	0	CD79B CL E G H	974	1699	OMIM:612692	Agammaglobulinemia 6, autosomal recessive		6
HP:0010976	HP:0010976	B lymphocytopenia	0	DCLRE1C CL E G H	64421	17642	OMIM:603554	Omenn syndrome	.	94
HP:0010976	HP:0010976	B lymphocytopenia	0	DCLRE1C CL E G H	64421	17642	OMIM:602450	Severe combined immunodeficiency with sensitivity to ionizing radiation		94
HP:0010976	HP:0010976	B lymphocytopenia	0	DOCK8 CL E G H	81704	19191	ORPHA:217390	Combined immunodeficiency due to DOCK8 deficiency	HP:0040281 - Very frequent	217
HP:0010976	HP:0010976	B lymphocytopenia	0	FCHO1 CL E G H	23149	29002	OMIM:619164	IMMUNODEFICIENCY 76; IMD76
HP:0010976	HP:0010976	B lymphocytopenia	0	FNIP1 CL E G H	96459	29418	OMIM:619705	IMMUNODEFICIENCY 93 AND HYPERTROPHIC CARDIOMYOPATHY; IMD93		1
HP:0010976	HP:0010976	B lymphocytopenia	0	GFI1 CL E G H	2672	4237	OMIM:613107	Neutropenia, severe congenital, 2, autosomal dominant	.	56
HP:0010976	HP:0010976	B lymphocytopenia	0	ICOS CL E G H	29851	5351	OMIM:607594	Immunodeficiency, common variable, 1		32
HP:0010976	HP:0010976	B lymphocytopenia	0	IGHM CL E G H	3507	5541	OMIM:601495	Agammaglobulinemia 1, autosomal recessive	.	7
HP:0010976	HP:0010976	B lymphocytopenia	0	IGLL1 CL E G H	3543	5870	OMIM:613500	Agammaglobulinemia 2, autosomal recessive		3
HP:0010976	HP:0010976	B lymphocytopenia	0	IKBKG CL E G H	8517	5961	OMIM:301081			52
HP:0010976	HP:0010976	B lymphocytopenia	0	IKZF1 CL E G H	10320	13176	OMIM:616873	IMMUNODEFICIENCY, COMMON VARIABLE, 13; CVID13		8
HP:0010976	HP:0010976	B lymphocytopenia	0	IKZF3 CL E G H	22806	13178	OMIM:619437	IMMUNODEFICIENCY 84; IMD84
HP:0010976	HP:0010976	B lymphocytopenia	0	IL2RA CL E G H	3559	6008	OMIM:606367	IMMUNODEFICIENCY 41 WITH LYMPHOPROLIFERATION AND AUTOIMMUNITY; IMD41		65
HP:0010976	HP:0010976	B lymphocytopenia	0	IVNS1ABP CL E G H	10625	16951	OMIM:618969	IMMUNODEFICIENCY 70; IMD70
HP:0010976	HP:0010976	B lymphocytopenia	0	JAK3 CL E G H	3718	6193	ORPHA:35078	T-B+ severe combined immunodeficiency due to JAK3 deficiency	HP:0040283 - Occasional	140
HP:0010976	HP:0010976	B lymphocytopenia	0	KNSTRN CL E G H	90417	30767	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	1
HP:0010976	HP:0010976	B lymphocytopenia	0	LRBA CL E G H	987	1742	OMIM:614700	IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY; CVID8		45
HP:0010976	HP:0010976	B lymphocytopenia	0	MCM10 CL E G H	55388	18043	OMIM:619313	IMMUNODEFICIENCY 80 WITH OR WITHOUT CONGENITAL CARDIOMYOPATHY; IMD80
HP:0010976	HP:0010976	B lymphocytopenia	0	MYD88 CL E G H	4615	7562	OMIM:612260	MYD88 DEFICIENCY; MYD88D		9
HP:0010976	HP:0010976	B lymphocytopenia	0	MYSM1 CL E G H	114803	29401	ORPHA:508542	Congenital progressive bone marrow failure-B-cell immunodeficiency-skeletal dysplasia syndrome	HP:0040282 - Frequent
HP:0010976	HP:0010976	B lymphocytopenia	0	NBN CL E G H	4683	7652	OMIM:251260	Nijmegen breakage syndrome	.	706
HP:0010976	HP:0010976	B lymphocytopenia	0	NFKB2 CL E G H	4791	7795	ORPHA:293978	Deficiency in anterior pituitary function-variable immunodeficiency syndrome		11
HP:0010976	HP:0010976	B lymphocytopenia	0	NHEJ1 CL E G H	79840	25737	ORPHA:169079	Cernunnos-XLF deficiency	HP:0040281 - Very frequent	20
HP:0010976	HP:0010976	B lymphocytopenia	0	PIK3CD CL E G H	5293	8977	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	9
HP:0010976	HP:0010976	B lymphocytopenia	0	PIK3CD CL E G H	5293	8977	OMIM:619281	IMMUNODEFICIENCY 14B, AUTOSOMAL RECESSIVE; IMD14B		9
HP:0010976	HP:0010976	B lymphocytopenia	0	PIK3R1 CL E G H	5295	8979	OMIM:616005	Immunodeficiency 36		43
HP:0010976	HP:0010976	B lymphocytopenia	0	POMP CL E G H	51371	20330	OMIM:618048	Proteasome-Associated autoinflammatory syndrome 2		2
HP:0010976	HP:0010976	B lymphocytopenia	0	PRIM1 CL E G H	5557	9369	OMIM:620005
HP:0010976	HP:0010976	B lymphocytopenia	0	RAC2 CL E G H	5880	9802	OMIM:618986	IMMUNODEFICIENCY 73B WITH DEFECTIVE NEUTROPHIL CHEMOTAXIS AND LYMPHOPENIA; IMD73B		9
HP:0010976	HP:0010976	B lymphocytopenia	0	RAC2 CL E G H	5880	9802	OMIM:618987	IMMUNODEFICIENCY 73C WITH DEFECTIVE NEUTROPHIL CHEMOTAXIS AND HYPOGAMMAGLOBULINEMIA; IMD73C		9
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG1 CL E G H	5896	9831	OMIM:233650	Combined cellular and humoral immune defects with granulomas	.	127
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG1 CL E G H	5896	9831	ORPHA:231154	Combined immunodeficiency due to partial RAG1 deficiency	HP:0040281 - Very frequent	127
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG1 CL E G H	5896	9831	OMIM:603554	Omenn syndrome	.	127
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG1 CL E G H	5896	9831	OMIM:601457	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	.	127
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG2 CL E G H	5897	9832	OMIM:233650	Combined cellular and humoral immune defects with granulomas	.	50
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG2 CL E G H	5897	9832	OMIM:603554	Omenn syndrome	.	50
HP:0010976	HP:0010976	B lymphocytopenia	0	RAG2 CL E G H	5897	9832	OMIM:601457	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	.	50
HP:0010976	HP:0010976	B lymphocytopenia	0	REL CL E G H	5966	9954	OMIM:619652	IMMUNODEFICIENCY 92; IMD92		1
HP:0010976	HP:0010976	B lymphocytopenia	0	RIPK1 CL E G H	8737	10019	OMIM:618108	IMMUNODEFICIENCY 57; IMD57
HP:0010976	HP:0010976	B lymphocytopenia	0	SASH3 CL E G H	54440	15975	OMIM:301082			1
HP:0010976	HP:0010976	B lymphocytopenia	0	SLC39A7 CL E G H	7922	4927	OMIM:619693	AGAMMAGLOBULINEMIA 9, AUTOSOMAL RECESSIVE; AGM9
HP:0010976	HP:0010976	B lymphocytopenia	0	SPI1 CL E G H	6688	11241	OMIM:619707	AGAMMAGLOBULINEMIA 10, AUTOSOMAL DOMINANT; AGM10
HP:0010976	HP:0010976	B lymphocytopenia	0	STAT1 CL E G H	6772	11362	ORPHA:391487	Autoimmune enteropathy and endocrinopathy-susceptibility to chronic infections syndrome	HP:0040282 - Frequent	89
HP:0010976	HP:0010976	B lymphocytopenia	0	SYK CL E G H	6850	11491	OMIM:619381	IMMUNODEFICIENCY 82 WITH SYSTEMIC INFLAMMATION; IMD82		1
HP:0010976	HP:0010976	B lymphocytopenia	0	TCF3 CL E G H	6929	11633	OMIM:616941	Agammaglobulinemia 8, autosomal dominant		2
HP:0010976	HP:0010976	B lymphocytopenia	0	TCF3 CL E G H	6929	11633	OMIM:619824	AGAMMAGLOBULINEMIA 8B, AUTOSOMAL RECESSIVE; AGM8B		2
HP:0010976	HP:0010976	B lymphocytopenia	0	TLR8 CL E G H	51311	15632	OMIM:301078	IMMUNODEFICIENCY 98 WITH AUTOINFLAMMATION, X-LINKED; IMD98
HP:0010976	HP:0010976	B lymphocytopenia	0	TOM1 CL E G H	10043	11982	ORPHA:391487	Autoimmune enteropathy and endocrinopathy-susceptibility to chronic infections syndrome	HP:0040282 - Frequent
HP:0010976	HP:0010976	B lymphocytopenia	0	TRNT1 CL E G H	51095	17341	OMIM:616084	SIDEROBLASTIC ANEMIA WITH B-CELL IMMUNODEFICIENCY, PERIODIC FEVERS, AND DEVELOPMENTAL DELAY; SIFD		28
HP:0010976	HP:0010976	B lymphocytopenia	0	UNC119 CL E G H	9094	12565	OMIM:615518	IMMUNODEFICIENCY 13; IMD13		30
HP:0010976	HP:0010976	B lymphocytopenia	0	WDR1 CL E G H	9948	12754	OMIM:150550	Periodic fever, immunodeficiency, and thrombocytopenia syndrome
HP:0010976	HP:0030251	Absence of memory B cells	1	CL E G H
HP:0010976	HP:0005365	Severe B lymphocytopenia	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:0010976	HP:0030252	Absent circulating B cells	1	BTK CL E G H	695	1133	OMIM:307200	Isolated growth hormone deficiency, type III, with agammaglobulinemia		109
HP:0010976	HP:0005365	Severe B lymphocytopenia	1	DCLRE1C CL E G H	64421	17642	OMIM:603554	Omenn syndrome	.	94
HP:0010976	HP:0030252	Absent circulating B cells	1	FNIP1 CL E G H	96459	29418	OMIM:619705	IMMUNODEFICIENCY 93 AND HYPERTROPHIC CARDIOMYOPATHY; IMD93		1
HP:0010976	HP:0030252	Absent circulating B cells	1	IGLL1 CL E G H	3543	5870	OMIM:613500	Agammaglobulinemia 2, autosomal recessive		3
HP:0010976	HP:0005365	Severe B lymphocytopenia	1	NFKB2 CL E G H	4791	7795	ORPHA:293978	Deficiency in anterior pituitary function-variable immunodeficiency syndrome	HP:0040281 - Very frequent	11
HP:0010976	HP:0005365	Severe B lymphocytopenia	1	PRIM1 CL E G H	5557	9369	OMIM:620005
HP:0010976	HP:0005365	Severe B lymphocytopenia	1	RAG1 CL E G H	5896	9831	OMIM:603554	Omenn syndrome	.	127
HP:0010976	HP:0005365	Severe B lymphocytopenia	1	RAG2 CL E G H	5897	9832	OMIM:603554	Omenn syndrome	.	50
HP:0010976	HP:0030252	Absent circulating B cells	1	SLC39A7 CL E G H	7922	4927	OMIM:619693	AGAMMAGLOBULINEMIA 9, AUTOSOMAL RECESSIVE; AGM9
HP:0010976	HP:0030252	Absent circulating B cells	1	SPI1 CL E G H	6688	11241	OMIM:619707	AGAMMAGLOBULINEMIA 10, AUTOSOMAL DOMINANT; AGM10

Genes (49) :ADA ALG12 ARHGEF1 ATP11A B2M BTK CD79B DCLRE1C DOCK8 FCHO1 FNIP1 GFI1 ICOS IGHM IGLL1 IKBKG IKZF1 IKZF3 IL2RA IVNS1ABP JAK3 KNSTRN LRBA MCM10 MYD88 MYSM1 NBN NFKB2 NHEJ1 PIK3CD PIK3R1 POMP PRIM1 RAC2 RAG1 RAG2 REL RIPK1 SASH3 SLC39A7 SPI1 STAT1 SYK TCF3 TLR8 TOM1 TRNT1 UNC119 WDR1

Diseases (54) :ORPHA:277 OMIM:102700 ORPHA:79324 OMIM:618459 OMIM:619851 OMIM:241600 OMIM:300755 OMIM:307200 OMIM:612692 OMIM:603554 OMIM:602450 ORPHA:217390 OMIM:619164 OMIM:619705 OMIM:613107 OMIM:607594 OMIM:601495 OMIM:613500 OMIM:301081 OMIM:616873 OMIM:619437 OMIM:606367 OMIM:618969 ORPHA:35078 ORPHA:221139 OMIM:614700 OMIM:619313 OMIM:612260 ORPHA:508542 OMIM:251260 ORPHA:293978 ORPHA:169079 OMIM:619281 OMIM:616005 OMIM:618048 OMIM:620005 OMIM:618986 OMIM:618987 OMIM:233650 ORPHA:231154 OMIM:601457 OMIM:619652 OMIM:618108 OMIM:301082 OMIM:619693 OMIM:619707 ORPHA:391487 OMIM:619381 OMIM:616941 OMIM:619824 OMIM:301078 OMIM:616084 OMIM:615518 OMIM:150550

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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