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 brain morphology (HP:0012443)

Parent Node:
Abnormal basal ganglia morphology (HP:0002134)

Parent Node:
Abnormal midbrain morphology (HP:0002418)

..Starting node
..Abnormal substantia nigra morphology (HP:0045007)

Term ID:

45007

Name:

Abnormal substantia nigra morphology

Synonym:

Abnormality of the substantia nigra

Definition:

A structural anomaly of the substantia nigra, which is a midbrain dopaminergic nucleus which has a critical role in modulating motor movement and reward functions as part of the basal ganglia circuitry.

Comments:

Reference:

HP:0045007

Genes and Diseases:

Child Nodes:

........

Substantia nigra gliosis (HP:0011960)

........

Iron accumulation in substantia nigra (HP:0012678)

Sister Nodes:

Absent mesencephalon (HP:0007265)

Molar tooth sign on MRI (HP:0002419)

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:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ADH1C CL E G H	126	251	OMIM:168600	Parkinson disease, late-onset		4
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN2 CL E G H	6311	10555	OMIM:168600	Parkinson disease, late-onset		11
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN2 CL E G H	6311	10555	ORPHA:98756	Spinocerebellar ataxia type 2	HP:0040281 - Very frequent	11
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN3 CL E G H	4287	7106	ORPHA:276238	Machado-Joseph disease type 1		14
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN3 CL E G H	4287	7106	ORPHA:276241	Machado-Joseph disease type 2		14
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN3 CL E G H	4287	7106	ORPHA:276244	Machado-Joseph disease type 3		14
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	ATXN8OS CL E G H	6315	10561	OMIM:168600	Parkinson disease, late-onset		1
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	C19ORF12 CL E G H	83636	25443	ORPHA:289560	Mitochondrial membrane protein-associated neurodegeneration	HP:0040282 - Frequent	114
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	FBXO7 CL E G H	25793	13586	ORPHA:171695	Parkinsonian-pyramidal syndrome		36
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	FTL CL E G H	2512	3999	ORPHA:157846	Neuroferritinopathy		33
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	GBA1 CL E G H	2629	4177	OMIM:168600	Parkinson disease, late-onset
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	GCH1 CL E G H	2643	4193	ORPHA:98808	Autosomal dominant dopa-responsive dystonia	HP:0040282 - Frequent	86
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	GLUD2 CL E G H	2747	4336	OMIM:168600	Parkinson disease, late-onset		1
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	GTPBP2 CL E G H	54676	4670	OMIM:617988	Jaberi-Elahi syndrome
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	IMPDH2 CL E G H	3615	6053	ORPHA:98808	Autosomal dominant dopa-responsive dystonia	HP:0040282 - Frequent	1
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	LRRK2 CL E G H	120892	18618	OMIM:607060	Parkinson disease 8, autosomal dominant		221
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	MAPT CL E G H	4137	6893	OMIM:168600	Parkinson disease, late-onset		140
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	NR4A2 CL E G H	4929	7981	OMIM:619911			27
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	NR4A2 CL E G H	4929	7981	ORPHA:98808	Autosomal dominant dopa-responsive dystonia	HP:0040282 - Frequent	27
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	NR4A2 CL E G H	4929	7981	OMIM:168600	Parkinson disease, late-onset		27
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	PRKN CL E G H	5071	8607	OMIM:600116	Parkinson disease, juvenile, type 2		138
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	SLC44A1 CL E G H	23446	18798	OMIM:618868	NEURODEGENERATION, CHILDHOOD-ONSET, WITH ATAXIA, TREMOR, OPTIC ATROPHY, AND COGNITIVE DECLINE; CONATOC		1
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	SNCA CL E G H	6622	11138	ORPHA:171695	Parkinsonian-pyramidal syndrome		65
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	SNCAIP CL E G H	9627	11139	OMIM:168600	Parkinson disease, late-onset		35
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	SPG11 CL E G H	80208	11226	ORPHA:2822	Autosomal recessive spastic paraplegia type 11	HP:0040283 - Occasional	287
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	TBCE CL E G H	6905	11582	ORPHA:496756	Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome		52
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	TBP CL E G H	6908	11588	OMIM:168600	Parkinson disease, late-onset		7
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	TRNT CL E G H	4576	7499	OMIM:168600	Parkinson disease, late-onset
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	VPS41 CL E G H	27072	12713	OMIM:619389	SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29
HP:0045007	HP:0045007	Abnormal substantia nigra morphology	0	WDR45 CL E G H	11152	28912	ORPHA:329284	Beta-propeller protein-associated neurodegeneration		51
HP:0045007	HP:0033249	Focal substantia nigra T2 hyperintensity	1	CL E G H
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ADH1C CL E G H	126	251	OMIM:168600	Parkinson disease, late-onset	.	4
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ATXN2 CL E G H	6311	10555	OMIM:168600	Parkinson disease, late-onset	.	11
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ATXN3 CL E G H	4287	7106	ORPHA:276238	Machado-Joseph disease type 1	HP:0040282 - Frequent	14
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ATXN3 CL E G H	4287	7106	ORPHA:276241	Machado-Joseph disease type 2	HP:0040282 - Frequent	14
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ATXN3 CL E G H	4287	7106	ORPHA:276244	Machado-Joseph disease type 3	HP:0040282 - Frequent	14
HP:0045007	HP:0011960	Substantia nigra gliosis	1	ATXN8OS CL E G H	6315	10561	OMIM:168600	Parkinson disease, late-onset	.	1
HP:0045007	HP:0011960	Substantia nigra gliosis	1	FBXO7 CL E G H	25793	13586	ORPHA:171695	Parkinsonian-pyramidal syndrome	HP:0040282 - Frequent	36
HP:0045007	HP:0012678	Iron accumulation in substantia nigra	1	FTL CL E G H	2512	3999	ORPHA:157846	Neuroferritinopathy	HP:0040282 - Frequent	33
HP:0045007	HP:0011960	Substantia nigra gliosis	1	GBA1 CL E G H	2629	4177	OMIM:168600	Parkinson disease, late-onset	.
HP:0045007	HP:0011960	Substantia nigra gliosis	1	GLUD2 CL E G H	2747	4336	OMIM:168600	Parkinson disease, late-onset	.	1
HP:0045007	HP:0033048	Substantia nigra hypointensity on susceptibility-weighted imaging	1	GTPBP2 CL E G H	54676	4670	OMIM:617988	Jaberi-Elahi syndrome
HP:0045007	HP:0011960	Substantia nigra gliosis	1	LRRK2 CL E G H	120892	18618	OMIM:607060	Parkinson disease 8, autosomal dominant	.	221
HP:0045007	HP:0011960	Substantia nigra gliosis	1	MAPT CL E G H	4137	6893	OMIM:168600	Parkinson disease, late-onset	.	140
HP:0045007	HP:0034316	Thinning of the substantia nigra pars compacta	1	NR4A2 CL E G H	4929	7981	OMIM:619911			27
HP:0045007	HP:0011960	Substantia nigra gliosis	1	NR4A2 CL E G H	4929	7981	OMIM:168600	Parkinson disease, late-onset	.	27
HP:0045007	HP:0011960	Substantia nigra gliosis	1	PRKN CL E G H	5071	8607	OMIM:600116	Parkinson disease, juvenile, type 2	.	138
HP:0045007	HP:0033048	Substantia nigra hypointensity on susceptibility-weighted imaging	1	SLC44A1 CL E G H	23446	18798	OMIM:618868	NEURODEGENERATION, CHILDHOOD-ONSET, WITH ATAXIA, TREMOR, OPTIC ATROPHY, AND COGNITIVE DECLINE; CONATOC		1
HP:0045007	HP:0011960	Substantia nigra gliosis	1	SNCA CL E G H	6622	11138	ORPHA:171695	Parkinsonian-pyramidal syndrome	HP:0040282 - Frequent	65
HP:0045007	HP:0011960	Substantia nigra gliosis	1	SNCAIP CL E G H	9627	11139	OMIM:168600	Parkinson disease, late-onset	.	35
HP:0045007	HP:0012678	Iron accumulation in substantia nigra	1	TBCE CL E G H	6905	11582	ORPHA:496756	Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome	HP:0040283 - Occasional	52
HP:0045007	HP:0011960	Substantia nigra gliosis	1	TBP CL E G H	6908	11588	OMIM:168600	Parkinson disease, late-onset	.	7
HP:0045007	HP:0011960	Substantia nigra gliosis	1	TRNT CL E G H	4576	7499	OMIM:168600	Parkinson disease, late-onset	.
HP:0045007	HP:0012678	Iron accumulation in substantia nigra	1	VPS41 CL E G H	27072	12713	OMIM:619389	SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29
HP:0045007	HP:0012678	Iron accumulation in substantia nigra	1	WDR45 CL E G H	11152	28912	ORPHA:329284	Beta-propeller protein-associated neurodegeneration	HP:0040282 - Frequent	51

Genes (25) :ADH1C ATXN2 ATXN3 ATXN8OS C19ORF12 FBXO7 FTL GBA1 GCH1 GLUD2 GTPBP2 IMPDH2 LRRK2 MAPT NR4A2 PRKN SLC44A1 SNCA SNCAIP SPG11 TBCE TBP TRNT VPS41 WDR45

Diseases (18) :OMIM:168600 ORPHA:98756 ORPHA:276238 ORPHA:276241 ORPHA:276244 ORPHA:289560 ORPHA:171695 ORPHA:157846 ORPHA:98808 OMIM:617988 OMIM:607060 OMIM:619911 OMIM:600116 OMIM:618868 ORPHA:2822 ORPHA:496756 OMIM:619389 ORPHA:329284

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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