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:
Abnormality of the menstrual cycle (HP:0000140)

Parent Node:
Amenorrhea (HP:0000141)

..Starting node
..Primary amenorrhea (HP:0000786)

Term ID:

786

Name:

Primary amenorrhea

Synonym:

Definition:

Comments:

Reference:

HP:0000786

Genes and Diseases:

Child Nodes:

Sister Nodes:

Secondary amenorrhea (HP:0000869)

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:0000786	HP:0000786	Primary amenorrhea	0	ANOS1 CL E G H	3730	6211	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	65
HP:0000786	HP:0000786	Primary amenorrhea	0	AR CL E G H	367	644	OMIM:300068	Androgen insensitivity syndrome	.	125
HP:0000786	HP:0000786	Primary amenorrhea	0	AR CL E G H	367	644	ORPHA:99429	Complete androgen insensitivity syndrome	HP:0040281 - Very frequent	125
HP:0000786	HP:0000786	Primary amenorrhea	0	AR CL E G H	367	644	ORPHA:90797	Partial androgen insensitivity syndrome	HP:0040283 - Occasional	125
HP:0000786	HP:0000786	Primary amenorrhea	0	AXL CL E G H	558	905	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.
HP:0000786	HP:0000786	Primary amenorrhea	0	BMP15 CL E G H	9210	1068	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	16
HP:0000786	HP:0000786	Primary amenorrhea	0	BMP15 CL E G H	9210	1068	OMIM:300510	Ovarian dysgenesis 2	.	16
HP:0000786	HP:0000786	Primary amenorrhea	0	BMPR1B CL E G H	658	1077	OMIM:609441	Acromesomelic dysplasia, Demirhan type	.	90
HP:0000786	HP:0000786	Primary amenorrhea	0	BNC1 CL E G H	646	1081	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	BRD4 CL E G H	23476	13575	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional
HP:0000786	HP:0000786	Primary amenorrhea	0	CAV1 CL E G H	857	1527	OMIM:612526	Lipodystrophy, congenital generalized, type 3	.	11
HP:0000786	HP:0000786	Primary amenorrhea	0	CCDC141 CL E G H	285025	26821	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.
HP:0000786	HP:0000786	Primary amenorrhea	0	CCDC141 CL E G H	285025	26821	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional
HP:0000786	HP:0000786	Primary amenorrhea	0	CDON CL E G H	50937	17104	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	200
HP:0000786	HP:0000786	Primary amenorrhea	0	CHD7 CL E G H	55636	20626	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	515
HP:0000786	HP:0000786	Primary amenorrhea	0	CHD7 CL E G H	55636	20626	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	515
HP:0000786	HP:0000786	Primary amenorrhea	0	CISD2 CL E G H	493856	24212	OMIM:604928	Wolfram syndrome 2	.	3
HP:0000786	HP:0000786	Primary amenorrhea	0	CLPP CL E G H	8192	2084	OMIM:614129	Perrault syndrome 3	.	13
HP:0000786	HP:0000786	Primary amenorrhea	0	CPE CL E G H	1363	2303	OMIM:619326	BDV SYNDROME; BDVS
HP:0000786	HP:0000786	Primary amenorrhea	0	CTDP1 CL E G H	9150	2498	OMIM:604168	Congenital cataracts, facial dysmorphism, and neuropathy	HP:0040283 - Occasional	17
HP:0000786	HP:0000786	Primary amenorrhea	0	CYB5A CL E G H	1528	2570	ORPHA:90796	46,XY disorder of sex development due to isolated 17,20-lyase deficiency	HP:0040281 - Very frequent	2
HP:0000786	HP:0000786	Primary amenorrhea	0	CYP17A1 CL E G H	1586	2593	ORPHA:90796	46,XY disorder of sex development due to isolated 17,20-lyase deficiency	HP:0040281 - Very frequent	53
HP:0000786	HP:0000786	Primary amenorrhea	0	CYP17A1 CL E G H	1586	2593	OMIM:202110	Adrenal hyperplasia, congenital, due to 17-alpha-hydroxylase deficiency	.	53
HP:0000786	HP:0000786	Primary amenorrhea	0	CYP17A1 CL E G H	1586	2593	ORPHA:90793	Congenital adrenal hyperplasia due to 17-alpha-hydroxylase deficiency	HP:0040282 - Frequent	53
HP:0000786	HP:0000786	Primary amenorrhea	0	CYP19A1 CL E G H	1588	2594	OMIM:613546	Aromatase deficiency	.	60
HP:0000786	HP:0000786	Primary amenorrhea	0	CYP19A1 CL E G H	1588	2594	ORPHA:91	Aromatase deficiency	HP:0040281 - Very frequent	60
HP:0000786	HP:0000786	Primary amenorrhea	0	DCC CL E G H	1630	2701	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	36
HP:0000786	HP:0000786	Primary amenorrhea	0	DHH CL E G H	50846	2865	OMIM:607080	46,XY GONADAL DYSGENESIS, PARTIAL, WITH MINIFASCICULAR NEUROPATHY		21
HP:0000786	HP:0000786	Primary amenorrhea	0	DHH CL E G H	50846	2865	ORPHA:168563	46,XY gonadal dysgenesis-motor and sensory neuropathy syndrome	HP:0040281 - Very frequent	21
HP:0000786	HP:0000786	Primary amenorrhea	0	DHH CL E G H	50846	2865	OMIM:233420	46,xy sex reversal 7	.	21
HP:0000786	HP:0000786	Primary amenorrhea	0	DHX37 CL E G H	57647	17210	OMIM:273250	46, XY sex reversal 11		2
HP:0000786	HP:0000786	Primary amenorrhea	0	DHX37 CL E G H	57647	17210	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	2
HP:0000786	HP:0000786	Primary amenorrhea	0	DMRT3 CL E G H	58524	13909	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	1
HP:0000786	HP:0000786	Primary amenorrhea	0	DUSP6 CL E G H	1848	3072	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	4
HP:0000786	HP:0000786	Primary amenorrhea	0	DUSP6 CL E G H	1848	3072	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	4
HP:0000786	HP:0000786	Primary amenorrhea	0	DUSP6 CL E G H	1848	3072	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	4
HP:0000786	HP:0000786	Primary amenorrhea	0	EIF2B1 CL E G H	1967	3257	OMIM:603896	Leukoencephalopathy with vanishing white matter	.	42
HP:0000786	HP:0000786	Primary amenorrhea	0	EIF2B2 CL E G H	8892	3258	OMIM:603896	Leukoencephalopathy with vanishing white matter	.	24
HP:0000786	HP:0000786	Primary amenorrhea	0	EIF2B3 CL E G H	8891	3259	OMIM:603896	Leukoencephalopathy with vanishing white matter	.	32
HP:0000786	HP:0000786	Primary amenorrhea	0	EIF2B4 CL E G H	8890	3260	OMIM:603896	Leukoencephalopathy with vanishing white matter	.	38
HP:0000786	HP:0000786	Primary amenorrhea	0	EIF2B5 CL E G H	8893	3261	OMIM:603896	Leukoencephalopathy with vanishing white matter	.	48
HP:0000786	HP:0000786	Primary amenorrhea	0	ERAL1 CL E G H	26284	3424	OMIM:617565	PERRAULT SYNDROME 6; PRLTS6		1
HP:0000786	HP:0000786	Primary amenorrhea	0	ESR1 CL E G H	2099	3467	OMIM:615363	Estrogen resistance	.	13
HP:0000786	HP:0000786	Primary amenorrhea	0	ESR1 CL E G H	2099	3467	ORPHA:785	Estrogen resistance syndrome	HP:0040281 - Very frequent	13
HP:0000786	HP:0000786	Primary amenorrhea	0	ESR2 CL E G H	2100	3468	OMIM:618187	Ovarian dysgenesis 8	.
HP:0000786	HP:0000786	Primary amenorrhea	0	FEZF1 CL E G H	389549	22788	OMIM:616030	Hypogonadotropic hypogonadism 22 with or without anosmia	.	2
HP:0000786	HP:0000786	Primary amenorrhea	0	FEZF1 CL E G H	389549	22788	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	2
HP:0000786	HP:0000786	Primary amenorrhea	0	FEZF1 CL E G H	389549	22788	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	2
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF17 CL E G H	8822	3673	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	3
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF17 CL E G H	8822	3673	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	3
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF17 CL E G H	8822	3673	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	3
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF8 CL E G H	2253	3686	OMIM:612702	Hypogonadotropic hypogonadism 6 with or without anosmia	.	17
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF8 CL E G H	2253	3686	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	17
HP:0000786	HP:0000786	Primary amenorrhea	0	FGF8 CL E G H	2253	3686	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	17
HP:0000786	HP:0000786	Primary amenorrhea	0	FGFR1 CL E G H	2260	3688	OMIM:147950	Hypogonadotropic hypogonadism 2 with or without anosmia	.	172
HP:0000786	HP:0000786	Primary amenorrhea	0	FGFR1 CL E G H	2260	3688	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	172
HP:0000786	HP:0000786	Primary amenorrhea	0	FGFR1 CL E G H	2260	3688	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	172
HP:0000786	HP:0000786	Primary amenorrhea	0	FIGLA CL E G H	344018	24669	OMIM:612310	PREMATURE OVARIAN FAILURE 6; POF6		17
HP:0000786	HP:0000786	Primary amenorrhea	0	FLRT3 CL E G H	23767	3762	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	4
HP:0000786	HP:0000786	Primary amenorrhea	0	FSHB CL E G H	2488	3964	OMIM:229070	Hypogonadotropic hypogonadism 24 without anosmia	.	23
HP:0000786	HP:0000786	Primary amenorrhea	0	FSHB CL E G H	2488	3964	ORPHA:52901	Isolated follicle stimulating hormone deficiency	HP:0040281 - Very frequent	23
HP:0000786	HP:0000786	Primary amenorrhea	0	FSHR CL E G H	2492	3969	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	50
HP:0000786	HP:0000786	Primary amenorrhea	0	FSHR CL E G H	2492	3969	OMIM:233300	Ovarian dysgenesis 1	.	50
HP:0000786	HP:0000786	Primary amenorrhea	0	GALT CL E G H	2592	4135	ORPHA:79239	Classic galactosemia	HP:0040282 - Frequent	351
HP:0000786	HP:0000786	Primary amenorrhea	0	GATA3 CL E G H	2625	4172	OMIM:146255	Hypoparathyroidism, sensorineural deafness, and renal dysplasia		83
HP:0000786	HP:0000786	Primary amenorrhea	0	GATA4 CL E G H	2626	4173	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	87
HP:0000786	HP:0000786	Primary amenorrhea	0	GDF9 CL E G H	2661	4224	OMIM:618014	Premature ovarian failure 14	.	2
HP:0000786	HP:0000786	Primary amenorrhea	0	GNRH1 CL E G H	2796	4419	OMIM:614841	Hypogonadotropic hypogonadism 12 with or without anosmia	.	15
HP:0000786	HP:0000786	Primary amenorrhea	0	GNRH1 CL E G H	2796	4419	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	15
HP:0000786	HP:0000786	Primary amenorrhea	0	GNRH1 CL E G H	2796	4419	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	15
HP:0000786	HP:0000786	Primary amenorrhea	0	GNRHR CL E G H	2798	4421	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	92
HP:0000786	HP:0000786	Primary amenorrhea	0	GNRHR CL E G H	2798	4421	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	92
HP:0000786	HP:0000786	Primary amenorrhea	0	GPR161 CL E G H	23432	23694	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	2
HP:0000786	HP:0000786	Primary amenorrhea	0	HDAC8 CL E G H	55869	13315	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional	37
HP:0000786	HP:0000786	Primary amenorrhea	0	HERC2 CL E G H	8924	4868	OMIM:176270	Prader-Willi syndrome		38
HP:0000786	HP:0000786	Primary amenorrhea	0	HESX1 CL E G H	8820	4877	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	21
HP:0000786	HP:0000786	Primary amenorrhea	0	HESX1 CL E G H	8820	4877	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	21
HP:0000786	HP:0000786	Primary amenorrhea	0	HS6ST1 CL E G H	9394	5201	OMIM:614880	Hypogonadotropic hypogonadism 15 with or without anosmia	.	8
HP:0000786	HP:0000786	Primary amenorrhea	0	HS6ST1 CL E G H	9394	5201	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	8
HP:0000786	HP:0000786	Primary amenorrhea	0	HS6ST1 CL E G H	9394	5201	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	8
HP:0000786	HP:0000786	Primary amenorrhea	0	HSD17B4 CL E G H	3295	5213	OMIM:233400	Perrault syndrome 1	.	98
HP:0000786	HP:0000786	Primary amenorrhea	0	IL17RD CL E G H	54756	17616	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	9
HP:0000786	HP:0000786	Primary amenorrhea	0	IPW CL E G H	3653	6109	OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	ITGA8 CL E G H	8516	6144	OMIM:191830	Renal hypodysplasia/aplasia 1	.	4
HP:0000786	HP:0000786	Primary amenorrhea	0	KISS1 CL E G H	3814	6341	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	3
HP:0000786	HP:0000786	Primary amenorrhea	0	KISS1R CL E G H	84634	4510	OMIM:614837	Hypogonadotropic hypogonadism 8 with or without anosmia	.	14
HP:0000786	HP:0000786	Primary amenorrhea	0	KISS1R CL E G H	84634	4510	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	14
HP:0000786	HP:0000786	Primary amenorrhea	0	LARS2 CL E G H	23395	17095	OMIM:615300	Perrault syndrome 4		54
HP:0000786	HP:0000786	Primary amenorrhea	0	LEP CL E G H	3952	6553	OMIM:614962	Leptin deficiency or dysfunction	.	47
HP:0000786	HP:0000786	Primary amenorrhea	0	LEP CL E G H	3952	6553	ORPHA:66628	Obesity due to congenital leptin deficiency	HP:0040281 - Very frequent	47
HP:0000786	HP:0000786	Primary amenorrhea	0	LEPR CL E G H	3953	6554	ORPHA:179494	Obesity due to leptin receptor gene deficiency	HP:0040281 - Very frequent	46
HP:0000786	HP:0000786	Primary amenorrhea	0	LHX4 CL E G H	89884	21734	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	43
HP:0000786	HP:0000786	Primary amenorrhea	0	MAGEL2 CL E G H	54551	6814	ORPHA:398069	MAGEL2-related Prader-Willi-like syndrome	HP:0040282 - Frequent	63
HP:0000786	HP:0000786	Primary amenorrhea	0	MAGEL2 CL E G H	54551	6814	OMIM:176270	Prader-Willi syndrome		63
HP:0000786	HP:0000786	Primary amenorrhea	0	MAGEL2 CL E G H	54551	6814	ORPHA:98754	Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	HP:0040282 - Frequent	63
HP:0000786	HP:0000786	Primary amenorrhea	0	MAGEL2 CL E G H	54551	6814	ORPHA:177901	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1	HP:0040282 - Frequent	63
HP:0000786	HP:0000786	Primary amenorrhea	0	MAGEL2 CL E G H	54551	6814	ORPHA:177904	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2	HP:0040282 - Frequent	63
HP:0000786	HP:0000786	Primary amenorrhea	0	MAP3K1 CL E G H	4214	6848	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	13
HP:0000786	HP:0000786	Primary amenorrhea	0	MCM8 CL E G H	84515	16147	OMIM:612885	Premature ovarian failure 10		4
HP:0000786	HP:0000786	Primary amenorrhea	0	MCM9 CL E G H	254394	21484	OMIM:616185	Ovarian dysgenesis 4	.	4
HP:0000786	HP:0000786	Primary amenorrhea	0	MKRN3 CL E G H	7681	7114	OMIM:176270	Prader-Willi syndrome		5
HP:0000786	HP:0000786	Primary amenorrhea	0	MKRN3-AS1 CL E G H	10108		OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	MRPS22 CL E G H	56945	14508	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	25
HP:0000786	HP:0000786	Primary amenorrhea	0	MRPS22 CL E G H	56945	14508	OMIM:618117	Ovarian dysgenesis 7	.	25
HP:0000786	HP:0000786	Primary amenorrhea	0	MSTO1 CL E G H	55154	29678	ORPHA:502423	Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	HP:0040282 - Frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	MSTO1 CL E G H	55154	29678	OMIM:617675	Myopathy, mitochondrial, and ataxia	.
HP:0000786	HP:0000786	Primary amenorrhea	0	NDN CL E G H	4692	7675	ORPHA:98754	Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	HP:0040282 - Frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	NDN CL E G H	4692	7675	ORPHA:177901	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1	HP:0040282 - Frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	NDN CL E G H	4692	7675	ORPHA:177904	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2	HP:0040282 - Frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	NDNF CL E G H	79625	26256	OMIM:618841	HYPOGONADOTROPIC HYPOGONADISM 25 WITH ANOSMIA; HH25
HP:0000786	HP:0000786	Primary amenorrhea	0	NDNF CL E G H	79625	26256	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional
HP:0000786	HP:0000786	Primary amenorrhea	0	NIN CL E G H	51199	14906	ORPHA:319675	Microcephalic primordial dwarfism, Dauber type	HP:0040282 - Frequent	55
HP:0000786	HP:0000786	Primary amenorrhea	0	NIN CL E G H	51199	14906	OMIM:614851	Seckel syndrome 7	.	55
HP:0000786	HP:0000786	Primary amenorrhea	0	NIPBL CL E G H	25836	28862	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional	494
HP:0000786	HP:0000786	Primary amenorrhea	0	NOBOX CL E G H	135935	22448	OMIM:611548	Premature ovarian failure 5	HP:0040283 - Occasional	40
HP:0000786	HP:0000786	Primary amenorrhea	0	NPAP1 CL E G H	23742	1190	OMIM:176270	Prader-Willi syndrome		1
HP:0000786	HP:0000786	Primary amenorrhea	0	NR0B1 CL E G H	190	7960	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	48
HP:0000786	HP:0000786	Primary amenorrhea	0	NR5A1 CL E G H	2516	7983	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	38
HP:0000786	HP:0000786	Primary amenorrhea	0	NR5A1 CL E G H	2516	7983	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	38
HP:0000786	HP:0000786	Primary amenorrhea	0	NR5A1 CL E G H	2516	7983	OMIM:612964	PREMATURE OVARIAN FAILURE 7; POF7		38
HP:0000786	HP:0000786	Primary amenorrhea	0	NSMF CL E G H	26012	29843	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	6
HP:0000786	HP:0000786	Primary amenorrhea	0	NUP107 CL E G H	57122	29914	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	5
HP:0000786	HP:0000786	Primary amenorrhea	0	OCA2 CL E G H	4948	8101	ORPHA:98754	Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	HP:0040282 - Frequent	121
HP:0000786	HP:0000786	Primary amenorrhea	0	OCA2 CL E G H	4948	8101	ORPHA:177901	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1	HP:0040282 - Frequent	121
HP:0000786	HP:0000786	Primary amenorrhea	0	OCA2 CL E G H	4948	8101	ORPHA:177904	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2	HP:0040282 - Frequent	121
HP:0000786	HP:0000786	Primary amenorrhea	0	PCSK1 CL E G H	5122	8743	OMIM:600955	Proprotein convertase 1/3 deficiency	.	65
HP:0000786	HP:0000786	Primary amenorrhea	0	PEX1 CL E G H	5189	8850	ORPHA:3220	Deafness-enamel hypoplasia-nail defects syndrome	HP:0040282 - Frequent	169
HP:0000786	HP:0000786	Primary amenorrhea	0	PEX6 CL E G H	5190	8859	ORPHA:3220	Deafness-enamel hypoplasia-nail defects syndrome	HP:0040282 - Frequent	98
HP:0000786	HP:0000786	Primary amenorrhea	0	POF1B CL E G H	79983	13711	OMIM:300604	Premature ovarian failure 2B	.	31
HP:0000786	HP:0000786	Primary amenorrhea	0	POLG CL E G H	5428	9179	OMIM:157640	Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1	.	464
HP:0000786	HP:0000786	Primary amenorrhea	0	POLR3H CL E G H	171568	30349	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	POR CL E G H	5447	9208	ORPHA:95699	Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency	HP:0040283 - Occasional	76
HP:0000786	HP:0000786	Primary amenorrhea	0	PPARG CL E G H	5468	9236	OMIM:604367	Lipodystrophy, familial partial, type 3	.	42
HP:0000786	HP:0000786	Primary amenorrhea	0	PPARG CL E G H	5468	9236	ORPHA:79083	PPARG-related familial partial lipodystrophy	HP:0040284 - Very rare	42
HP:0000786	HP:0000786	Primary amenorrhea	0	PROK2 CL E G H	60675	18455	OMIM:610628	Hypogonadotropic hypogonadism 4 with or without anosmia	.	9
HP:0000786	HP:0000786	Primary amenorrhea	0	PROK2 CL E G H	60675	18455	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	9
HP:0000786	HP:0000786	Primary amenorrhea	0	PROK2 CL E G H	60675	18455	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	9
HP:0000786	HP:0000786	Primary amenorrhea	0	PROKR2 CL E G H	128674	15836	OMIM:244200	Hypogonadotropic hypogonadism 3 with or without anosmia	.	34
HP:0000786	HP:0000786	Primary amenorrhea	0	PROKR2 CL E G H	128674	15836	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	34
HP:0000786	HP:0000786	Primary amenorrhea	0	PROKR2 CL E G H	128674	15836	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	34
HP:0000786	HP:0000786	Primary amenorrhea	0	PROKR2 CL E G H	128674	15836	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	34
HP:0000786	HP:0000786	Primary amenorrhea	0	PRORP CL E G H	9692	19958	OMIM:619737	COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 54; COXPD54
HP:0000786	HP:0000786	Primary amenorrhea	0	PSMC3IP CL E G H	29893	17928	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	2
HP:0000786	HP:0000786	Primary amenorrhea	0	PSMC3IP CL E G H	29893	17928	OMIM:614324	Ovarian dysgenesis 3	.	2
HP:0000786	HP:0000786	Primary amenorrhea	0	PWAR1 CL E G H	145624	30089	OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	PWRN1 CL E G H	791114	33235	OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	RAD21 CL E G H	5885	9811	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional	25
HP:0000786	HP:0000786	Primary amenorrhea	0	ROBO1 CL E G H	6091	10249	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	7
HP:0000786	HP:0000786	Primary amenorrhea	0	SEMA3A CL E G H	10371	10723	OMIM:614897	Hypogonadotropic hypogonadism 16 with or without anosmia	.	14
HP:0000786	HP:0000786	Primary amenorrhea	0	SEMA3A CL E G H	10371	10723	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	14
HP:0000786	HP:0000786	Primary amenorrhea	0	SEMA3E CL E G H	9723	10727	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	16
HP:0000786	HP:0000786	Primary amenorrhea	0	SIM1 CL E G H	6492	10882	ORPHA:398079	SIM1-related Prader-Willi-like syndrome	HP:0040282 - Frequent	40
HP:0000786	HP:0000786	Primary amenorrhea	0	SMC1A CL E G H	8243	11111	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional	135
HP:0000786	HP:0000786	Primary amenorrhea	0	SMC3 CL E G H	9126	2468	ORPHA:199	Cornelia de Lange syndrome	HP:0040283 - Occasional	91
HP:0000786	HP:0000786	Primary amenorrhea	0	SMCHD1 CL E G H	23347	29090	OMIM:603457	Bosma arhinia microphthalmia syndrome		174
HP:0000786	HP:0000786	Primary amenorrhea	0	SNORD115-1 CL E G H	338433	33020	OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	SNORD116-1 CL E G H	100033413	33067	OMIM:176270	Prader-Willi syndrome
HP:0000786	HP:0000786	Primary amenorrhea	0	SNRPN CL E G H	6638	11164	ORPHA:98754	Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	HP:0040282 - Frequent	37
HP:0000786	HP:0000786	Primary amenorrhea	0	SNRPN CL E G H	6638	11164	ORPHA:177901	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1	HP:0040282 - Frequent	37
HP:0000786	HP:0000786	Primary amenorrhea	0	SNRPN CL E G H	6638	11164	ORPHA:177904	Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2	HP:0040282 - Frequent	37
HP:0000786	HP:0000786	Primary amenorrhea	0	SOHLH1 CL E G H	402381	27845	OMIM:617690	Ovarian dysgenesis 5	.	3
HP:0000786	HP:0000786	Primary amenorrhea	0	SOX10 CL E G H	6663	11190	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	61
HP:0000786	HP:0000786	Primary amenorrhea	0	SOX9 CL E G H	6662	11204	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	109
HP:0000786	HP:0000786	Primary amenorrhea	0	SPIDR CL E G H	23514	28971	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent	2
HP:0000786	HP:0000786	Primary amenorrhea	0	SPIDR CL E G H	23514	28971	OMIM:619665	OVARIAN DYSGENESIS 9; ODG9		2
HP:0000786	HP:0000786	Primary amenorrhea	0	SPRY4 CL E G H	81848	15533	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	5
HP:0000786	HP:0000786	Primary amenorrhea	0	SPRY4 CL E G H	81848	15533	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	5
HP:0000786	HP:0000786	Primary amenorrhea	0	SPRY4 CL E G H	81848	15533	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	5
HP:0000786	HP:0000786	Primary amenorrhea	0	SRA1 CL E G H	10011	11281	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.
HP:0000786	HP:0000786	Primary amenorrhea	0	SRY CL E G H	6736	11311	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	23
HP:0000786	HP:0000786	Primary amenorrhea	0	SRY CL E G H	6736	11311	OMIM:400044	46XY sex reversal 1	.	23
HP:0000786	HP:0000786	Primary amenorrhea	0	STAG3 CL E G H	10734	11356	OMIM:615723	Premature ovarian failure 8	.	4
HP:0000786	HP:0000786	Primary amenorrhea	0	SYCE1 CL E G H	93426	28852	OMIM:616947	PREMATURE OVARIAN FAILURE 12; POF12		4
HP:0000786	HP:0000786	Primary amenorrhea	0	TAC3 CL E G H	6866	11521	OMIM:614839	Hypogonadotropic hypogonadism 10 with or without anosmia	.	6
HP:0000786	HP:0000786	Primary amenorrhea	0	TAC3 CL E G H	6866	11521	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	6
HP:0000786	HP:0000786	Primary amenorrhea	0	TACR3 CL E G H	6870	11528	OMIM:614840	Hypogonadotropic hypogonadism 11 with or without anosmia	.	34
HP:0000786	HP:0000786	Primary amenorrhea	0	TACR3 CL E G H	6870	11528	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	34
HP:0000786	HP:0000786	Primary amenorrhea	0	TACR3 CL E G H	6870	11528	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	34
HP:0000786	HP:0000786	Primary amenorrhea	0	TP63 CL E G H	8626	15979	ORPHA:69085	Limb-mammary syndrome	HP:0040284 - Very rare	140
HP:0000786	HP:0000786	Primary amenorrhea	0	TRMT10A CL E G H	93587	28403	OMIM:616033	Microcephaly, short stature, and impaired glucose metabolism 1	HP:0040283 - Occasional	7
HP:0000786	HP:0000786	Primary amenorrhea	0	TWNK CL E G H	56652	1160	OMIM:616138	Perrault syndrome 5	.	113
HP:0000786	HP:0000786	Primary amenorrhea	0	VAMP7 CL E G H	6845	11486	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	2
HP:0000786	HP:0000786	Primary amenorrhea	0	WDR11 CL E G H	55717	13831	OMIM:614858	Hypogonadotropic hypogonadism 14 with or without anosmia	.	10
HP:0000786	HP:0000786	Primary amenorrhea	0	WDR11 CL E G H	55717	13831	OMIM:146110	Hypogonadotropic hypogonadism 7 without anosmia	.	10
HP:0000786	HP:0000786	Primary amenorrhea	0	WDR11 CL E G H	55717	13831	ORPHA:478	Kallmann syndrome	HP:0040283 - Occasional	10
HP:0000786	HP:0000786	Primary amenorrhea	0	WDR11 CL E G H	55717	13831	ORPHA:432	Normosmic congenital hypogonadotropic hypogonadism	HP:0040281 - Very frequent	10
HP:0000786	HP:0000786	Primary amenorrhea	0	WDR11 CL E G H	55717	13831	ORPHA:95496	Pituitary stalk interruption syndrome	HP:0040283 - Occasional	10
HP:0000786	HP:0000786	Primary amenorrhea	0	WNT4 CL E G H	54361	12783	ORPHA:247768	Müllerian aplasia and hyperandrogenism	HP:0040281 - Very frequent	4
HP:0000786	HP:0000786	Primary amenorrhea	0	WT1 CL E G H	7490	12796	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	177
HP:0000786	HP:0000786	Primary amenorrhea	0	WT1 CL E G H	7490	12796	ORPHA:347	Frasier syndrome	HP:0040281 - Very frequent	177
HP:0000786	HP:0000786	Primary amenorrhea	0	WT1 CL E G H	7490	12796	OMIM:136680	Frasier syndrome		177
HP:0000786	HP:0000786	Primary amenorrhea	0	WWOX CL E G H	51741	12799	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	149
HP:0000786	HP:0000786	Primary amenorrhea	0	YARS1 CL E G H	8565	12840	OMIM:619418	NEUROLOGIC, ENDOCRINE, AND PANCREATIC DISEASE, MULTISYSTEM, INFANTILE-ONSET 2; IMNEPD2
HP:0000786	HP:0000786	Primary amenorrhea	0	ZFPM2 CL E G H	23414	16700	ORPHA:251510	46,XY partial gonadal dysgenesis	HP:0040281 - Very frequent	31
HP:0000786	HP:0000786	Primary amenorrhea	0	ZSWIM7 CL E G H	125150	26993	ORPHA:243	46,XX gonadal dysgenesis	HP:0040281 - Very frequent
HP:0000786	HP:0000786	Primary amenorrhea	0	ZSWIM7 CL E G H	125150	26993	OMIM:619834	OVARIAN DYSGENESIS 10; ODG10

Genes (126) :ANOS1 AR AXL BMP15 BMPR1B BNC1 BRD4 CAV1 CCDC141 CDON CHD7 CISD2 CLPP CPE CTDP1 CYB5A CYP17A1 CYP19A1 DCC DHH DHX37 DMRT3 DUSP6 EIF2B1 EIF2B2 EIF2B3 EIF2B4 EIF2B5 ERAL1 ESR1 ESR2 FEZF1 FGF17 FGF8 FGFR1 FIGLA FLRT3 FSHB FSHR GALT GATA3 GATA4 GDF9 GNRH1 GNRHR GPR161 HDAC8 HERC2 HESX1 HS6ST1 HSD17B4 IL17RD IPW ITGA8 KISS1 KISS1R LARS2 LEP LEPR LHX4 MAGEL2 MAP3K1 MCM8 MCM9 MKRN3 MKRN3-AS1 MRPS22 MSTO1 NDN NDNF NIN NIPBL NOBOX NPAP1 NR0B1 NR5A1 NSMF NUP107 OCA2 PCSK1 PEX1 PEX6 POF1B POLG POLR3H POR PPARG PROK2 PROKR2 PRORP PSMC3IP PWAR1 PWRN1 RAD21 ROBO1 SEMA3A SEMA3E SIM1 SMC1A SMC3 SMCHD1 SNORD115-1 SNORD116-1 SNRPN SOHLH1 SOX10 SOX9 SPIDR SPRY4 SRA1 SRY STAG3 SYCE1 TAC3 TACR3 TP63 TRMT10A TWNK VAMP7 WDR11 WNT4 WT1 WWOX YARS1 ZFPM2 ZSWIM7

Diseases (95) :ORPHA:478 OMIM:300068 ORPHA:99429 ORPHA:90797 OMIM:146110 ORPHA:243 OMIM:300510 OMIM:609441 ORPHA:199 OMIM:612526 ORPHA:95496 ORPHA:432 OMIM:604928 OMIM:614129 OMIM:619326 OMIM:604168 ORPHA:90796 OMIM:202110 ORPHA:90793 OMIM:613546 ORPHA:91 OMIM:607080 ORPHA:168563 OMIM:233420 OMIM:273250 ORPHA:251510 OMIM:603896 OMIM:617565 OMIM:615363 ORPHA:785 OMIM:618187 OMIM:616030 OMIM:612702 OMIM:147950 OMIM:612310 OMIM:229070 ORPHA:52901 OMIM:233300 ORPHA:79239 OMIM:146255 OMIM:618014 OMIM:614841 OMIM:176270 OMIM:614880 OMIM:233400 OMIM:191830 OMIM:614837 OMIM:615300 OMIM:614962 ORPHA:66628 ORPHA:179494 ORPHA:398069 ORPHA:98754 ORPHA:177901 ORPHA:177904 OMIM:612885 OMIM:616185 OMIM:618117 ORPHA:502423 OMIM:617675 OMIM:618841 ORPHA:319675 OMIM:614851 OMIM:611548 OMIM:612964 OMIM:600955 ORPHA:3220 OMIM:300604 OMIM:157640 ORPHA:95699 OMIM:604367 ORPHA:79083 OMIM:610628 OMIM:244200 OMIM:619737 OMIM:614324 OMIM:614897 ORPHA:398079 OMIM:603457 OMIM:617690 OMIM:619665 OMIM:400044 OMIM:615723 OMIM:616947 OMIM:614839 OMIM:614840 ORPHA:69085 OMIM:616033 OMIM:616138 OMIM:614858 ORPHA:247768 ORPHA:347 OMIM:136680 OMIM:619418 OMIM:619834

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