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:
Functional abnormality of male internal genitalia (HP:0000025)

Parent Node:
Abnormal spermatogenesis (HP:0008669)

..Starting node
..Oligospermia (HP:0000798)

Term ID:

798

Name:

Oligospermia

Synonym:

Low sperm count

Definition:

Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen.

Comments:

Reference:

HP:0000798

Genes and Diseases:

Child Nodes:

........

Cryptozoospermia (HP:0030974)

Sister Nodes:

Azoospermia (HP:0000027)

Spermatogenesis maturation arrest (HP:0031038)

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:0000798	HP:0000798	Oligospermia	0	ADGRG2 CL E G H	10149	4516	ORPHA:48	Congenital bilateral absence of vas deferens	HP:0040283 - Occasional	5
HP:0000798	HP:0000798	Oligospermia	0	ALMS1 CL E G H	7840	428	ORPHA:64	Alström syndrome	HP:0040283 - Occasional	404
HP:0000798	HP:0000798	Oligospermia	0	ANTXR1 CL E G H	84168	21014	ORPHA:2067	GAPO syndrome	HP:0040283 - Occasional	8
HP:0000798	HP:0000798	Oligospermia	0	ARMC2 CL E G H	84071	23045	OMIM:618433	SPERMATOGENIC FAILURE 38; SPGF38
HP:0000798	HP:0000798	Oligospermia	0	BLM CL E G H	641	1058	ORPHA:125	Bloom syndrome	HP:0040283 - Occasional	314
HP:0000798	HP:0000798	Oligospermia	0	CATIP CL E G H	375307	25062	OMIM:619379	SPERMATOGENIC FAILURE 54; SPGF54
HP:0000798	HP:0000798	Oligospermia	0	CATSPER1 CL E G H	117144	17116	OMIM:612997	Spermatogenic failure 7	.	45
HP:0000798	HP:0000798	Oligospermia	0	CATSPER2 CL E G H	117155	18810	OMIM:612997	Spermatogenic failure 7	.	12
HP:0000798	HP:0000798	Oligospermia	0	CCDC34 CL E G H	91057	25079	OMIM:620084
HP:0000798	HP:0000798	Oligospermia	0	CEP19 CL E G H	84984	28209	OMIM:615703	Morbid obesity and spermatogenic failure		1
HP:0000798	HP:0000798	Oligospermia	0	CFAP47 CL E G H	286464	26708	OMIM:301059	SPERMATOGENIC FAILURE, X-LINKED, 3; SPGFX3		1
HP:0000798	HP:0000798	Oligospermia	0	CFAP65 CL E G H	255101	25325	OMIM:618664	SPERMATOGENIC FAILURE 40; SPGF40		1
HP:0000798	HP:0000798	Oligospermia	0	CFAP70 CL E G H	118491	30726	OMIM:618670	SPERMATOGENIC FAILURE 41; SPGF41
HP:0000798	HP:0000798	Oligospermia	0	CFAP91 CL E G H	89876	24010	OMIM:619177	SPERMATOGENIC FAILURE 51; SPGF51
HP:0000798	HP:0000798	Oligospermia	0	CFTR CL E G H	1080	1884	ORPHA:48	Congenital bilateral absence of vas deferens	HP:0040283 - Occasional	1371
HP:0000798	HP:0000798	Oligospermia	0	CNBP CL E G H	7555	13164	OMIM:602668	Dystrophia myotonica 2	.	1
HP:0000798	HP:0000798	Oligospermia	0	DAZ1 CL E G H	1617	2682	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	DAZ2 CL E G H	57055	15964	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	DAZ3 CL E G H	57054	15965	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	DAZ4 CL E G H	57135	15966	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	DDX3Y CL E G H	8653	2699	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	DNAH10 CL E G H	196385	2941	OMIM:619515	SPERMATOGENIC FAILURE 56; SPGF56		18
HP:0000798	HP:0000798	Oligospermia	0	DNAH17 CL E G H	8632	2946	OMIM:618643	SPERMATOGENIC FAILURE 39; SPGF39		37
HP:0000798	HP:0000798	Oligospermia	0	DNHD1 CL E G H	144132	26532	OMIM:619712	SPERMATOGENIC FAILURE 65; SPGF65
HP:0000798	HP:0000798	Oligospermia	0	DZIP1 CL E G H	22873	20908	OMIM:619102	SPERMATOGENIC FAILURE 47; SPGF47
HP:0000798	HP:0000798	Oligospermia	0	FBXO43 CL E G H	286151	28521	OMIM:619696	SPERMATOGENIC FAILURE 64; SPGF64
HP:0000798	HP:0000798	Oligospermia	0	FKBP6 CL E G H	8468	3722	OMIM:620103
HP:0000798	HP:0000798	Oligospermia	0	FSHB CL E G H	2488	3964	ORPHA:52901	Isolated follicle stimulating hormone deficiency	HP:0040282 - Frequent	23
HP:0000798	HP:0000798	Oligospermia	0	IFT74 CL E G H	80173	21424	OMIM:619585	SPERMATOGENIC FAILURE 58; SPGF58		3
HP:0000798	HP:0000798	Oligospermia	0	KLHL10 CL E G H	317719	18829	OMIM:615081	SPERMATOGENIC FAILURE 11; SPGF11		3
HP:0000798	HP:0000798	Oligospermia	0	LHCGR CL E G H	3973	6585	ORPHA:3000	Familial male-limited precocious puberty	HP:0040283 - Occasional	67
HP:0000798	HP:0000798	Oligospermia	0	M1AP CL E G H	130951	25183	OMIM:619108	SPERMATOGENIC FAILURE 48; SPGF48
HP:0000798	HP:0000798	Oligospermia	0	MEIOB CL E G H	254528	28569	OMIM:617706	Spermatogenic failure 22
HP:0000798	HP:0000798	Oligospermia	0	MSH4 CL E G H	4438	7327	OMIM:108420	Spermatogenic failure 2	.
HP:0000798	HP:0000798	Oligospermia	0	NR0B1 CL E G H	190	7960	OMIM:300200	Adrenal hypoplasia, congenital	.	48
HP:0000798	HP:0000798	Oligospermia	0	NR3C1 CL E G H	2908	7978	ORPHA:786	Generalized glucocorticoid resistance syndrome	HP:0040283 - Occasional	79
HP:0000798	HP:0000798	Oligospermia	0	NR5A1 CL E G H	2516	7983	OMIM:613957	Spermatogenic failure 8	.	38
HP:0000798	HP:0000798	Oligospermia	0	PDE11A CL E G H	50940	8773	ORPHA:1359	Carney complex		13
HP:0000798	HP:0000798	Oligospermia	0	PDHA2 CL E G H	5161	8807	OMIM:619828	SPERMATOGENIC FAILURE 70; SPGF70
HP:0000798	HP:0000798	Oligospermia	0	PMFBP1 CL E G H	83449	17728	ORPHA:529970	Male infertility due to acephalic spermatozoa	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	POC1A CL E G H	25886	24488	OMIM:614813	Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis	.	10
HP:0000798	HP:0000798	Oligospermia	0	POR CL E G H	5447	9208	ORPHA:95699	Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency	HP:0040282 - Frequent	76
HP:0000798	HP:0000798	Oligospermia	0	PRKAR1A CL E G H	5573	9388	ORPHA:1359	Carney complex		134
HP:0000798	HP:0000798	Oligospermia	0	RBMY1A1 CL E G H	5940	9912	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	RPL10L CL E G H	140801	17976	OMIM:619689	SPERMATOGENIC FAILURE 63; SPGF63		2
HP:0000798	HP:0000798	Oligospermia	0	STRC CL E G H	161497	16035	OMIM:612997	Spermatogenic failure 7	.	78
HP:0000798	HP:0000798	Oligospermia	0	SUN5 CL E G H	140732	16252	ORPHA:529970	Male infertility due to acephalic spermatozoa	HP:0040282 - Frequent	6
HP:0000798	HP:0000798	Oligospermia	0	SYCP2 CL E G H	10388	11490	OMIM:258150	SPERMATOGENIC FAILURE 1; SPGF1		1
HP:0000798	HP:0000798	Oligospermia	0	TDRD9 CL E G H	122402	20122	OMIM:618110	Spermatogenic failure 30
HP:0000798	HP:0000798	Oligospermia	0	TEX15 CL E G H	56154	11738	OMIM:617960	Spermatogenic failure 25		1
HP:0000798	HP:0000798	Oligospermia	0	TSPY1 CL E G H	7258	12381	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent
HP:0000798	HP:0000798	Oligospermia	0	USP9Y CL E G H	8287	12633	ORPHA:1646	Partial chromosome Y deletion	HP:0040282 - Frequent	2
HP:0000798	HP:0030974	Cryptozoospermia	1	CATIP CL E G H	375307	25062	OMIM:619379	SPERMATOGENIC FAILURE 54; SPGF54
HP:0000798	HP:0030974	Cryptozoospermia	1	MEIOB CL E G H	254528	28569	OMIM:617706	Spermatogenic failure 22
HP:0000798	HP:0030974	Cryptozoospermia	1	NR5A1 CL E G H	2516	7983	OMIM:613957	Spermatogenic failure 8	.	38
HP:0000798	HP:0030974	Cryptozoospermia	1	SYCP2 CL E G H	10388	11490	OMIM:258150	SPERMATOGENIC FAILURE 1; SPGF1		1
HP:0000798	HP:0030974	Cryptozoospermia	1	TDRD9 CL E G H	122402	20122	OMIM:618110	Spermatogenic failure 30	.
HP:0000798	HP:0030974	Cryptozoospermia	1	TEX15 CL E G H	56154	11738	OMIM:617960	Spermatogenic failure 25	.	1

Genes (52) :ADGRG2 ALMS1 ANTXR1 ARMC2 BLM CATIP CATSPER1 CATSPER2 CCDC34 CEP19 CFAP47 CFAP65 CFAP70 CFAP91 CFTR CNBP DAZ1 DAZ2 DAZ3 DAZ4 DDX3Y DNAH10 DNAH17 DNHD1 DZIP1 FBXO43 FKBP6 FSHB IFT74 KLHL10 LHCGR M1AP MEIOB MSH4 NR0B1 NR3C1 NR5A1 PDE11A PDHA2 PMFBP1 POC1A POR PRKAR1A RBMY1A1 RPL10L STRC SUN5 SYCP2 TDRD9 TEX15 TSPY1 USP9Y

Diseases (40) :ORPHA:48 ORPHA:64 ORPHA:2067 OMIM:618433 ORPHA:125 OMIM:619379 OMIM:612997 OMIM:620084 OMIM:615703 OMIM:301059 OMIM:618664 OMIM:618670 OMIM:619177 OMIM:602668 ORPHA:1646 OMIM:619515 OMIM:618643 OMIM:619712 OMIM:619102 OMIM:619696 OMIM:620103 ORPHA:52901 OMIM:619585 OMIM:615081 ORPHA:3000 OMIM:619108 OMIM:617706 OMIM:108420 OMIM:300200 ORPHA:786 OMIM:613957 ORPHA:1359 OMIM:619828 ORPHA:529970 OMIM:614813 ORPHA:95699 OMIM:619689 OMIM:258150 OMIM:618110 OMIM:617960

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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