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:
External genital hypoplasia (HP:0003241)

Parent Node:
Abnormality of the scrotum (HP:0000045)

Parent Node:
Hypoplastic male external genitalia (HP:0000050)

..Starting node
..Small scrotum (HP:0000046)

Term ID:

Name:

Small scrotum

Synonym:

Hypoplastic scrotum; Scrotal hypoplasia; Smaller than typical growth of scrotum; Underdeveloped scrotum

Definition:

Apparently small scrotum for age.

Comments:

Reference:

HP:0000046

Genes and Diseases:

Child Nodes:

Sister Nodes:

Decreased testicular size (HP:0008734)

Hypoplasia of penis (HP:0008736)

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:0000046	HP:0000046	Small scrotum	0	ALG12 CL E G H	79087	19358	OMIM:607143	Congenital disorder of glycosylation, type Ig	.	68
HP:0000046	HP:0000046	Small scrotum	0	ALX4 CL E G H	60529	450	ORPHA:228390	Frontonasal dysplasia-alopecia-genital anomalies syndrome	HP:0040282 - Frequent	132
HP:0000046	HP:0000046	Small scrotum	0	ANOS1 CL E G H	3730	6211	OMIM:308700	Hypogonadotropic hypogonadism 1 with or without anosmia		65
HP:0000046	HP:0000046	Small scrotum	0	ARCN1 CL E G H	372	649	OMIM:617164	Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay	.	3
HP:0000046	HP:0000046	Small scrotum	0	ATRX CL E G H	546	886	OMIM:309580	Mental retardation-hypotonic facies syndrome, X-linked, 1	.	169
HP:0000046	HP:0000046	Small scrotum	0	BLTP1 CL E G H	84162	26953	OMIM:617822	Alkuraya-Kucinskas syndrome	.
HP:0000046	HP:0000046	Small scrotum	0	BMP4 CL E G H	652	1071	OMIM:607932	Microphthalmia, syndromic 6		38
HP:0000046	HP:0000046	Small scrotum	0	CHRNG CL E G H	1146	1967	ORPHA:2990	Autosomal recessive multiple pterygium syndrome	HP:0040283 - Occasional	68
HP:0000046	HP:0000046	Small scrotum	0	CILK1 CL E G H	22858	21219	OMIM:612651	ENDOCRINE-CEREBROOSTEODYSPLASIA	.
HP:0000046	HP:0000046	Small scrotum	0	DHCR7 CL E G H	1717	2860	OMIM:270400	Smith-Lemli-Opitz syndrome		159
HP:0000046	HP:0000046	Small scrotum	0	ERCC2 CL E G H	2068	3434	OMIM:610756	Cerebrooculofacioskeletal syndrome 2		106
HP:0000046	HP:0000046	Small scrotum	0	FARSB CL E G H	10056	17800	OMIM:613658	Rajab interstitial lung disease with brain calcifications
HP:0000046	HP:0000046	Small scrotum	0	FRAS1 CL E G H	80144	19185	ORPHA:2052	Fraser syndrome	HP:0040282 - Frequent	353
HP:0000046	HP:0000046	Small scrotum	0	FREM2 CL E G H	341640	25396	ORPHA:2052	Fraser syndrome	HP:0040282 - Frequent	263
HP:0000046	HP:0000046	Small scrotum	0	GLI3 CL E G H	2737	4319	ORPHA:672	Pallister-Hall syndrome	HP:0040284 - Very rare	270
HP:0000046	HP:0000046	Small scrotum	0	GRIP1 CL E G H	23426	18708	ORPHA:2052	Fraser syndrome	HP:0040282 - Frequent	80
HP:0000046	HP:0000046	Small scrotum	0	GRIP1 CL E G H	23426	18708	OMIM:617667	Fraser syndrome 3	.	80
HP:0000046	HP:0000046	Small scrotum	0	HERC2 CL E G H	8924	4868	OMIM:176270	Prader-Willi syndrome		38
HP:0000046	HP:0000046	Small scrotum	0	IER3IP1 CL E G H	51124	18550	OMIM:614231	Microcephaly, epilepsy, and diabetes syndrome	HP:0040283 - Occasional	6
HP:0000046	HP:0000046	Small scrotum	0	IPW CL E G H	3653	6109	OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	0	IRF6 CL E G H	3664	6121	ORPHA:1300	Autosomal dominant popliteal pterygium syndrome	HP:0040282 - Frequent	99
HP:0000046	HP:0000046	Small scrotum	0	IRF6 CL E G H	3664	6121	OMIM:119500	Popliteal pterygium syndrome	.	99
HP:0000046	HP:0000046	Small scrotum	0	KAT6B CL E G H	23522	17582	ORPHA:85201	Genitopatellar syndrome	HP:0040281 - Very frequent	141
HP:0000046	HP:0000046	Small scrotum	0	KAT6B CL E G H	23522	17582	OMIM:606170	Genitopatellar syndrome	.	141
HP:0000046	HP:0000046	Small scrotum	0	LMX1B CL E G H	4010	6654	ORPHA:495818	9q33.3q34.11 microdeletion syndrome	HP:0040283 - Occasional	165
HP:0000046	HP:0000046	Small scrotum	0	MAGEL2 CL E G H	54551	6814	ORPHA:398069	MAGEL2-related Prader-Willi-like syndrome	HP:0040282 - Frequent	63
HP:0000046	HP:0000046	Small scrotum	0	MAGEL2 CL E G H	54551	6814	OMIM:176270	Prader-Willi syndrome		63
HP:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	0	MAPRE2 CL E G H	10982	6891	ORPHA:2505	Multiple benign circumferential skin creases on limbs	HP:0040283 - Occasional	4
HP:0000046	HP:0000046	Small scrotum	0	MAPRE2 CL E G H	10982	6891	OMIM:616734	Skin creases, congenital symmetric circumferential, 2	.	4
HP:0000046	HP:0000046	Small scrotum	0	MED12 CL E G H	9968	11957	OMIM:300895	Ohdo syndrome, X-linked	.	228
HP:0000046	HP:0000046	Small scrotum	0	MKRN3 CL E G H	7681	7114	OMIM:176270	Prader-Willi syndrome		5
HP:0000046	HP:0000046	Small scrotum	0	MKRN3-AS1 CL E G H	10108		OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	0	MYH3 CL E G H	4621	7573	ORPHA:2990	Autosomal recessive multiple pterygium syndrome	HP:0040283 - Occasional	166
HP:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	0	NECTIN1 CL E G H	5818	9706	ORPHA:3253	Cleft lip/palate-ectodermal dysplasia syndrome	HP:0040282 - Frequent	4
HP:0000046	HP:0000046	Small scrotum	0	NPAP1 CL E G H	23742	1190	OMIM:176270	Prader-Willi syndrome		1
HP:0000046	HP:0000046	Small scrotum	0	NR5A1 CL E G H	2516	7983	ORPHA:2138	46,XX ovotesticular disorder of sex development	HP:0040281 - Very frequent	38
HP:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	0	OPHN1 CL E G H	4983	8148	OMIM:300486	Mental retardation, X-linked, with cerebellar hypoplasia and distinctive facial appearance	.	55
HP:0000046	HP:0000046	Small scrotum	0	ORC6 CL E G H	23594	17151	OMIM:613803	Meier-Gorlin syndrome 3	.	39
HP:0000046	HP:0000046	Small scrotum	0	PHF6 CL E G H	84295	18145	ORPHA:127	Borjeson-Forssman-Lehmann syndrome	HP:0040281 - Very frequent	29
HP:0000046	HP:0000046	Small scrotum	0	PNPLA6 CL E G H	10908	16268	OMIM:245800	Laurence-Moon syndrome	.	103
HP:0000046	HP:0000046	Small scrotum	0	POLR1B CL E G H	84172	20454	ORPHA:861	Treacher-Collins syndrome	HP:0040283 - Occasional
HP:0000046	HP:0000046	Small scrotum	0	POLR1C CL E G H	9533	20194	ORPHA:861	Treacher-Collins syndrome	HP:0040283 - Occasional	38
HP:0000046	HP:0000046	Small scrotum	0	POLR1D CL E G H	51082	20422	ORPHA:861	Treacher-Collins syndrome	HP:0040283 - Occasional	31
HP:0000046	HP:0000046	Small scrotum	0	POR CL E G H	5447	9208	OMIM:201750	Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis	.	76
HP:0000046	HP:0000046	Small scrotum	0	PWAR1 CL E G H	145624	30089	OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	0	PWRN1 CL E G H	791114	33235	OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	0	RAB18 CL E G H	22931	14244	OMIM:614222	Warburg micro syndrome 3	.	85
HP:0000046	HP:0000046	Small scrotum	0	RAB3GAP2 CL E G H	25782	17168	OMIM:614225	Warburg micro syndrome 2	.	135
HP:0000046	HP:0000046	Small scrotum	0	RYR1 CL E G H	6261	10483	ORPHA:98905	Congenital multicore myopathy with external ophthalmoplegia	HP:0040283 - Occasional	1200
HP:0000046	HP:0000046	Small scrotum	0	SETBP1 CL E G H	26040	15573	OMIM:269150	Schinzel-Giedion midface-retraction syndrome	.	143
HP:0000046	HP:0000046	Small scrotum	0	SIM1 CL E G H	6492	10882	ORPHA:398079	SIM1-related Prader-Willi-like syndrome	HP:0040282 - Frequent	40
HP:0000046	HP:0000046	Small scrotum	0	SLC25A24 CL E G H	29957	20662	OMIM:612289	Fontaine progeroid syndrome	.
HP:0000046	HP:0000046	Small scrotum	0	SMARCA2 CL E G H	6595	11098	ORPHA:2728	Blepharophimosis-intellectual disability syndrome, Ohdo type	HP:0040281 - Very frequent	146
HP:0000046	HP:0000046	Small scrotum	0	SNORD115-1 CL E G H	338433	33020	OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	0	SNORD116-1 CL E G H	100033413	33067	OMIM:176270	Prader-Willi syndrome
HP:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	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:0000046	HP:0000046	Small scrotum	0	SOX9 CL E G H	6662	11204	ORPHA:2138	46,XX ovotesticular disorder of sex development	HP:0040281 - Very frequent	109
HP:0000046	HP:0000046	Small scrotum	0	SRD5A2 CL E G H	6716	11285	ORPHA:753	46,XY disorder of sex development due to 5-alpha-reductase 2 deficiency	HP:0040281 - Very frequent	86
HP:0000046	HP:0000046	Small scrotum	0	SRY CL E G H	6736	11311	ORPHA:2138	46,XX ovotesticular disorder of sex development	HP:0040281 - Very frequent	23
HP:0000046	HP:0000046	Small scrotum	0	STT3A CL E G H	3703	6172	ORPHA:370921	STT3A-CDG	HP:0040282 - Frequent	21
HP:0000046	HP:0000046	Small scrotum	0	STT3B CL E G H	201595	30611	OMIM:615597	Congenital disorder of glycosylation, type Ix	.	18
HP:0000046	HP:0000046	Small scrotum	0	STT3B CL E G H	201595	30611	ORPHA:370924	STT3B-CDG	HP:0040282 - Frequent	18
HP:0000046	HP:0000046	Small scrotum	0	STXBP1 CL E G H	6812	11444	ORPHA:495818	9q33.3q34.11 microdeletion syndrome	HP:0040283 - Occasional	237
HP:0000046	HP:0000046	Small scrotum	0	TBC1D20 CL E G H	128637	16133	OMIM:615663	Warburg micro syndrome 4		15
HP:0000046	HP:0000046	Small scrotum	0	TBX3 CL E G H	6926	11602	OMIM:181450	Ulnar-Mammary syndrome		100
HP:0000046	HP:0000046	Small scrotum	0	TCOF1 CL E G H	6949	11654	ORPHA:861	Treacher-Collins syndrome	HP:0040283 - Occasional	140
HP:0000046	HP:0000046	Small scrotum	0	TRRAP CL E G H	8295	12347	OMIM:618454	Developmental delay with or without dysmorphic facies and autism	.	2
HP:0000046	HP:0000046	Small scrotum	0	TSPYL1 CL E G H	7259	12382	ORPHA:168593	Sudden infant death-dysgenesis of the testes syndrome	HP:0040281 - Very frequent	1
HP:0000046	HP:0000046	Small scrotum	0	TUBB CL E G H	203068	20778	ORPHA:2505	Multiple benign circumferential skin creases on limbs	HP:0040283 - Occasional	14
HP:0000046	HP:0000046	Small scrotum	0	WNT7A CL E G H	7476	12786	OMIM:276820	Ulna and fibula, absence of, with severe limb deficiency		13

Genes (66) :ALG12 ALX4 ANOS1 ARCN1 ATRX BLTP1 BMP4 CHRNG CILK1 DHCR7 ERCC2 FARSB FRAS1 FREM2 GLI3 GRIP1 HERC2 IER3IP1 IPW IRF6 KAT6B LMX1B MAGEL2 MAPRE2 MED12 MKRN3 MKRN3-AS1 MYH3 NDN NECTIN1 NPAP1 NR5A1 OCA2 OPHN1 ORC6 PHF6 PNPLA6 POLR1B POLR1C POLR1D POR PWAR1 PWRN1 RAB18 RAB3GAP2 RYR1 SETBP1 SIM1 SLC25A24 SMARCA2 SNORD115-1 SNORD116-1 SNRPN SOX9 SRD5A2 SRY STT3A STT3B STXBP1 TBC1D20 TBX3 TCOF1 TRRAP TSPYL1 TUBB WNT7A

Diseases (53) :OMIM:607143 ORPHA:228390 OMIM:308700 OMIM:617164 OMIM:309580 OMIM:617822 OMIM:607932 ORPHA:2990 OMIM:612651 OMIM:270400 OMIM:610756 OMIM:613658 ORPHA:2052 ORPHA:672 OMIM:617667 OMIM:176270 OMIM:614231 ORPHA:1300 OMIM:119500 ORPHA:85201 OMIM:606170 ORPHA:495818 ORPHA:398069 ORPHA:98754 ORPHA:177901 ORPHA:177904 ORPHA:2505 OMIM:616734 OMIM:300895 ORPHA:3253 ORPHA:2138 OMIM:300486 OMIM:613803 ORPHA:127 OMIM:245800 ORPHA:861 OMIM:201750 OMIM:614222 OMIM:614225 ORPHA:98905 OMIM:269150 ORPHA:398079 OMIM:612289 ORPHA:2728 ORPHA:753 ORPHA:370921 OMIM:615597 ORPHA:370924 OMIM:615663 OMIM:181450 OMIM:618454 ORPHA:168593 OMIM:276820

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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