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:
Abnormality of immune system physiology (HP:0010978)

Parent Node:
Immunodeficiency (HP:0002721)

..Starting node
..Combined immunodeficiency (HP:0005387)

Term ID:

5387

Name:

Combined immunodeficiency

Synonym:

Definition:

A group of phenotypically heterogeneous genetic disorders characterized by profound deficiencies of T- and B-cell function, which predispose the patients to both infectious and noninfectious complications.

Comments:

Reference:

HP:0005387

Genes and Diseases:

Child Nodes:

........

Severe combined immunodeficiency (HP:0004430)

Sister Nodes:

Cellular immunodeficiency (HP:0005374)

Humoral immunodeficiency (HP:0005363)

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:0005387	HP:0005387	Combined immunodeficiency	0	ACP5 CL E G H	54	124	OMIM:607944	Spondyloenchondrodysplasia with immune dysregulation	.	16
HP:0005387	HP:0005387	Combined immunodeficiency	0	ADA CL E G H	100	186	ORPHA:39041	Omenn syndrome		75
HP:0005387	HP:0005387	Combined immunodeficiency	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:0005387	HP:0005387	Combined immunodeficiency	0	AK2 CL E G H	204	362	OMIM:267500	Reticular dysgenesia		19
HP:0005387	HP:0005387	Combined immunodeficiency	0	AK2 CL E G H	204	362	ORPHA:33355	Reticular dysgenesis		19
HP:0005387	HP:0005387	Combined immunodeficiency	0	BCL11B CL E G H	64919	13222	OMIM:617237	Immunodeficiency 49		3
HP:0005387	HP:0005387	Combined immunodeficiency	0	BUB1B CL E G H	701	1149	OMIM:257300	Mosaic variegated aneuploidy syndrome 1	.	76
HP:0005387	HP:0005387	Combined immunodeficiency	0	CD19 CL E G H	930	1633	OMIM:240500	Immunodeficiency, common variable, 2		38
HP:0005387	HP:0005387	Combined immunodeficiency	0	CD19 CL E G H	930	1633	OMIM:613493	IMMUNODEFICIENCY, COMMON VARIABLE, 3; CVID3		38
HP:0005387	HP:0005387	Combined immunodeficiency	0	CHD7 CL E G H	55636	20626	ORPHA:39041	Omenn syndrome		515
HP:0005387	HP:0005387	Combined immunodeficiency	0	CR2 CL E G H	1380	2336	OMIM:240500	Immunodeficiency, common variable, 2		10
HP:0005387	HP:0005387	Combined immunodeficiency	0	DCLRE1C CL E G H	64421	17642	ORPHA:39041	Omenn syndrome		94
HP:0005387	HP:0005387	Combined immunodeficiency	0	DCLRE1C CL E G H	64421	17642	OMIM:602450	Severe combined immunodeficiency with sensitivity to ionizing radiation		94
HP:0005387	HP:0005387	Combined immunodeficiency	0	DOCK2 CL E G H	1794	2988	OMIM:616433	Immunodeficiency 40		6
HP:0005387	HP:0005387	Combined immunodeficiency	0	EXTL3 CL E G H	2137	3518	OMIM:617425	Immunoskeletal dysplasia with neurodevelopmental abnormalities		3
HP:0005387	HP:0005387	Combined immunodeficiency	0	EXTL3 CL E G H	2137	3518	ORPHA:508533	Skeletal dysplasia-T-cell immunodeficiency-developmental delay syndrome		3
HP:0005387	HP:0005387	Combined immunodeficiency	0	ICOS CL E G H	29851	5351	OMIM:240500	Immunodeficiency, common variable, 2		32
HP:0005387	HP:0005387	Combined immunodeficiency	0	IKZF1 CL E G H	10320	13176	OMIM:616873	IMMUNODEFICIENCY, COMMON VARIABLE, 13; CVID13		8
HP:0005387	HP:0005387	Combined immunodeficiency	0	IL2RG CL E G H	3561	6010	OMIM:312863	Combined immunodeficiency, X-linked	.	48
HP:0005387	HP:0005387	Combined immunodeficiency	0	IL2RG CL E G H	3561	6010	ORPHA:39041	Omenn syndrome		48
HP:0005387	HP:0005387	Combined immunodeficiency	0	IL2RG CL E G H	3561	6010	OMIM:300400	Severe combined immunodeficiency, X-linked		48
HP:0005387	HP:0005387	Combined immunodeficiency	0	IL7R CL E G H	3575	6024	ORPHA:39041	Omenn syndrome		94
HP:0005387	HP:0005387	Combined immunodeficiency	0	IL7R CL E G H	3575	6024	OMIM:608971	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive		94
HP:0005387	HP:0005387	Combined immunodeficiency	0	IRF2BP2 CL E G H	359948	21729	OMIM:617765	IMMUNODEFICIENCY, COMMON VARIABLE, 14; CVID14		4
HP:0005387	HP:0005387	Combined immunodeficiency	0	JAK3 CL E G H	3718	6193	OMIM:600802	Scid, autosomal recessive, T-Negative/b-Positive type		140
HP:0005387	HP:0005387	Combined immunodeficiency	0	KNSTRN CL E G H	90417	30767	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	1
HP:0005387	HP:0005387	Combined immunodeficiency	0	LIG4 CL E G H	3981	6601	ORPHA:99812	LIG4 syndrome		88
HP:0005387	HP:0005387	Combined immunodeficiency	0	LIG4 CL E G H	3981	6601	ORPHA:39041	Omenn syndrome		88
HP:0005387	HP:0005387	Combined immunodeficiency	0	MGAT2 CL E G H	4247	7045	ORPHA:79329	MGAT2-CDG	HP:0040283 - Occasional	39
HP:0005387	HP:0005387	Combined immunodeficiency	0	MS4A1 CL E G H	931	7315	OMIM:613495	Immunodeficiency, common variable, 5		1
HP:0005387	HP:0005387	Combined immunodeficiency	0	MTHFD1 CL E G H	4522	7432	OMIM:617780	Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia		5
HP:0005387	HP:0005387	Combined immunodeficiency	0	NFKB1 CL E G H	4790	7794	OMIM:616576	IMMUNODEFICIENCY, COMMON VARIABLE, 12; CVID12		7
HP:0005387	HP:0005387	Combined immunodeficiency	0	NFKB2 CL E G H	4791	7795	OMIM:615577	Immunodeficiency, common variable, 10		11
HP:0005387	HP:0005387	Combined immunodeficiency	0	PGM3 CL E G H	5238	8907	ORPHA:443811	PGM3-CDG		15
HP:0005387	HP:0005387	Combined immunodeficiency	0	PI4KA CL E G H	5297	8983	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum		11
HP:0005387	HP:0005387	Combined immunodeficiency	0	PIK3CD CL E G H	5293	8977	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	9
HP:0005387	HP:0005387	Combined immunodeficiency	0	PNP CL E G H	4860	7892	ORPHA:760	Purine nucleoside phosphorylase deficiency		52
HP:0005387	HP:0005387	Combined immunodeficiency	0	PRKDC CL E G H	5591	9413	OMIM:615966	Immunodeficiency 26 with or without neurologic abnormalities		42
HP:0005387	HP:0005387	Combined immunodeficiency	0	RAG1 CL E G H	5896	9831	OMIM:233650	Combined cellular and humoral immune defects with granulomas	.	127
HP:0005387	HP:0005387	Combined immunodeficiency	0	RAG1 CL E G H	5896	9831	ORPHA:231154	Combined immunodeficiency due to partial RAG1 deficiency		127
HP:0005387	HP:0005387	Combined immunodeficiency	0	RAG1 CL E G H	5896	9831	ORPHA:39041	Omenn syndrome		127
HP:0005387	HP:0005387	Combined immunodeficiency	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:0005387	HP:0005387	Combined immunodeficiency	0	RAG2 CL E G H	5897	9832	OMIM:233650	Combined cellular and humoral immune defects with granulomas	.	50
HP:0005387	HP:0005387	Combined immunodeficiency	0	RAG2 CL E G H	5897	9832	ORPHA:39041	Omenn syndrome		50
HP:0005387	HP:0005387	Combined immunodeficiency	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:0005387	HP:0005387	Combined immunodeficiency	0	RMRP CL E G H	6023	10031	ORPHA:39041	Omenn syndrome		37
HP:0005387	HP:0005387	Combined immunodeficiency	0	TNFRSF13B CL E G H	23495	18153	OMIM:240500	Immunodeficiency, common variable, 2		32
HP:0005387	HP:0005387	Combined immunodeficiency	0	TNFRSF13C CL E G H	115650	17755	OMIM:240500	Immunodeficiency, common variable, 2		12
HP:0005387	HP:0005387	Combined immunodeficiency	0	TNFRSF13C CL E G H	115650	17755	OMIM:613494	Immunodeficiency, common variable, 4		12
HP:0005387	HP:0005387	Combined immunodeficiency	0	TTC7A CL E G H	57217	19750	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum		26
HP:0005387	HP:0005387	Combined immunodeficiency	0	TTC7A CL E G H	57217	19750	OMIM:243150	Gastrointestinal defects and immunodeficiency syndrome		26
HP:0005387	HP:0005387	Combined immunodeficiency	0	XRCC4 CL E G H	7518	12831	ORPHA:99812	LIG4 syndrome		9
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	ADA CL E G H	100	186	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	75
HP:0005387	HP:0004430	Severe combined immunodeficiency	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:0005387	HP:0004430	Severe combined immunodeficiency	1	AK2 CL E G H	204	362	ORPHA:33355	Reticular dysgenesis	HP:0040281 - Very frequent	19
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	BCL11B CL E G H	64919	13222	OMIM:617237	Immunodeficiency 49	.	3
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	CHD7 CL E G H	55636	20626	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	515
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	DCLRE1C CL E G H	64421	17642	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	94
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	DCLRE1C CL E G H	64421	17642	OMIM:602450	Severe combined immunodeficiency with sensitivity to ionizing radiation	.	94
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	EXTL3 CL E G H	2137	3518	OMIM:617425	Immunoskeletal dysplasia with neurodevelopmental abnormalities		3
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	EXTL3 CL E G H	2137	3518	ORPHA:508533	Skeletal dysplasia-T-cell immunodeficiency-developmental delay syndrome	HP:0040283 - Occasional	3
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	IL2RG CL E G H	3561	6010	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	48
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	IL2RG CL E G H	3561	6010	OMIM:300400	Severe combined immunodeficiency, X-linked		48
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	IL7R CL E G H	3575	6024	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	94
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	IL7R CL E G H	3575	6024	OMIM:608971	Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive	.	94
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	JAK3 CL E G H	3718	6193	OMIM:600802	Scid, autosomal recessive, T-Negative/b-Positive type		140
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	LIG4 CL E G H	3981	6601	ORPHA:99812	LIG4 syndrome	HP:0040282 - Frequent	88
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	LIG4 CL E G H	3981	6601	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	88
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	MTHFD1 CL E G H	4522	7432	OMIM:617780	Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia	.	5
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	PGM3 CL E G H	5238	8907	ORPHA:443811	PGM3-CDG	HP:0040283 - Occasional	15
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	PI4KA CL E G H	5297	8983	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum	HP:0040281 - Very frequent	11
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	PNP CL E G H	4860	7892	ORPHA:760	Purine nucleoside phosphorylase deficiency	HP:0040282 - Frequent	52
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	PRKDC CL E G H	5591	9413	OMIM:615966	Immunodeficiency 26 with or without neurologic abnormalities	.	42
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	RAG1 CL E G H	5896	9831	ORPHA:231154	Combined immunodeficiency due to partial RAG1 deficiency	HP:0040281 - Very frequent	127
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	RAG1 CL E G H	5896	9831	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	127
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	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:0005387	HP:0004430	Severe combined immunodeficiency	1	RAG2 CL E G H	5897	9832	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	50
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	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:0005387	HP:0004430	Severe combined immunodeficiency	1	RMRP CL E G H	6023	10031	ORPHA:39041	Omenn syndrome	HP:0040281 - Very frequent	37
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	TTC7A CL E G H	57217	19750	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum	HP:0040281 - Very frequent	26
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	TTC7A CL E G H	57217	19750	OMIM:243150	Gastrointestinal defects and immunodeficiency syndrome	HP:0040283 - Occasional	26
HP:0005387	HP:0004430	Severe combined immunodeficiency	1	XRCC4 CL E G H	7518	12831	ORPHA:99812	LIG4 syndrome	HP:0040282 - Frequent	9

Genes (36) :ACP5 ADA AK2 BCL11B BUB1B CD19 CHD7 CR2 DCLRE1C DOCK2 EXTL3 ICOS IKZF1 IL2RG IL7R IRF2BP2 JAK3 KNSTRN LIG4 MGAT2 MS4A1 MTHFD1 NFKB1 NFKB2 PGM3 PI4KA PIK3CD PNP PRKDC RAG1 RAG2 RMRP TNFRSF13B TNFRSF13C TTC7A XRCC4

Diseases (35) :OMIM:607944 ORPHA:39041 OMIM:102700 OMIM:267500 ORPHA:33355 OMIM:617237 OMIM:257300 OMIM:240500 OMIM:613493 OMIM:602450 OMIM:616433 OMIM:617425 ORPHA:508533 OMIM:616873 OMIM:312863 OMIM:300400 OMIM:608971 OMIM:617765 OMIM:600802 ORPHA:221139 ORPHA:99812 ORPHA:79329 OMIM:613495 OMIM:617780 OMIM:616576 OMIM:615577 ORPHA:443811 ORPHA:436252 ORPHA:760 OMIM:615966 OMIM:233650 ORPHA:231154 OMIM:601457 OMIM:613494 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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