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:
Aplasia/Hypoplasia of the thumb (HP:0009601)

Grandparent Node:
Short finger (HP:0009381)

Parent Node:
Aplasia/Hypoplasia of the phalanges of the thumb (HP:0009658)

Parent Node:
Short thumb (HP:0009778)

..Starting node
..Short phalanx of the thumb (HP:0009660)

Term ID:

9660

Name:

Short phalanx of the thumb

Synonym:

Hypoplastic thumb phalanges; Hypoplastic/small phalanges of the thumb; Short thumb bone; Short thumb phalanges

Definition:

Hypoplastic (short) thumb phalanx.

Comments:

Reference:

HP:0009660

Genes and Diseases:

Child Nodes:

........

Short proximal phalanx of thumb (HP:0009638)

........

Short distal phalanx of the thumb (HP:0009650)

........

Short 1st metacarpal (HP:0010034)

Sister Nodes:

Thumbs hypoplastic with bulbous tips (HP:0005726)

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:0009660	HP:0009660	Short phalanx of the thumb	0	ACVR1 CL E G H	90	171	OMIM:135100	Fibrodysplasia ossificans progressiva		49
HP:0009660	HP:0009660	Short phalanx of the thumb	0	BMPR1B CL E G H	658	1077	OMIM:609441	Acromesomelic dysplasia, Demirhan type		90
HP:0009660	HP:0009660	Short phalanx of the thumb	0	BMPR1B CL E G H	658	1077	OMIM:616849	BRACHYDACTYLY, TYPE A1, D; BDA1D		90
HP:0009660	HP:0009660	Short phalanx of the thumb	0	BRD4 CL E G H	23476	13575	ORPHA:199	Cornelia de Lange syndrome
HP:0009660	HP:0009660	Short phalanx of the thumb	0	CANT1 CL E G H	124583	19721	OMIM:251450	Desbuquois dysplasia 1		85
HP:0009660	HP:0009660	Short phalanx of the thumb	0	DLK1 CL E G H	8788	2907	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14		1
HP:0009660	HP:0009660	Short phalanx of the thumb	0	FANCI CL E G H	55215	25568	OMIM:609053	Fanconi anemia, complementation group I		157
HP:0009660	HP:0009660	Short phalanx of the thumb	0	FLNA CL E G H	2316	3754	ORPHA:1826	Frontometaphyseal dysplasia		493
HP:0009660	HP:0009660	Short phalanx of the thumb	0	FZD2 CL E G H	2535	4040	ORPHA:93328	Autosomal dominant omodysplasia
HP:0009660	HP:0009660	Short phalanx of the thumb	0	FZD2 CL E G H	2535	4040	OMIM:164745	OMODYSPLASIA
HP:0009660	HP:0009660	Short phalanx of the thumb	0	GDF5 CL E G H	8200	4220	ORPHA:63442	Angel-shaped phalango-epiphyseal dysplasia		52
HP:0009660	HP:0009660	Short phalanx of the thumb	0	GDF5 CL E G H	8200	4220	OMIM:113100	Brachydactyly, type C		52
HP:0009660	HP:0009660	Short phalanx of the thumb	0	GNAS CL E G H	2778	4392	ORPHA:79445	Pseudopseudohypoparathyroidism		101
HP:0009660	HP:0009660	Short phalanx of the thumb	0	HDAC8 CL E G H	55869	13315	ORPHA:199	Cornelia de Lange syndrome		37
HP:0009660	HP:0009660	Short phalanx of the thumb	0	HOXA13 CL E G H	3209	5102	OMIM:140000	Hand-Foot-Genital syndrome		11
HP:0009660	HP:0009660	Short phalanx of the thumb	0	HOXA13 CL E G H	3209	5102	ORPHA:2438	Hand-foot-genital syndrome		11
HP:0009660	HP:0009660	Short phalanx of the thumb	0	IHH CL E G H	3549	5956	OMIM:607778	Acrocapitofemoral dysplasia		44
HP:0009660	HP:0009660	Short phalanx of the thumb	0	IHH CL E G H	3549	5956	OMIM:112500	Brachydactyly, type A1		44
HP:0009660	HP:0009660	Short phalanx of the thumb	0	KCNH1 CL E G H	3756	6250	ORPHA:420561	Temple-Baraitser syndrome	HP:0040283 - Occasional	13
HP:0009660	HP:0009660	Short phalanx of the thumb	0	KNSTRN CL E G H	90417	30767	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies		1
HP:0009660	HP:0009660	Short phalanx of the thumb	0	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0009660	HP:0009660	Short phalanx of the thumb	0	MAP3K7 CL E G H	6885	6859	ORPHA:1826	Frontometaphyseal dysplasia		11
HP:0009660	HP:0009660	Short phalanx of the thumb	0	MEG3 CL E G H	55384	14575	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14		1
HP:0009660	HP:0009660	Short phalanx of the thumb	0	NIPBL CL E G H	25836	28862	ORPHA:199	Cornelia de Lange syndrome		494
HP:0009660	HP:0009660	Short phalanx of the thumb	0	NOG CL E G H	9241	7866	OMIM:611377	Brachydactyly, type B2		22
HP:0009660	HP:0009660	Short phalanx of the thumb	0	NOG CL E G H	9241	7866	OMIM:186570	Tarsal-Carpal coalition syndrome		22
HP:0009660	HP:0009660	Short phalanx of the thumb	0	PCNT CL E G H	5116	16068	OMIM:210720	Microcephalic osteodysplastic primordial dwarfism, type II		531
HP:0009660	HP:0009660	Short phalanx of the thumb	0	PIK3CD CL E G H	5293	8977	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies		9
HP:0009660	HP:0009660	Short phalanx of the thumb	0	PTCH1 CL E G H	5727	9585	OMIM:109400	Basal cell nevus syndrome		665
HP:0009660	HP:0009660	Short phalanx of the thumb	0	PTCH2 CL E G H	8643	9586	OMIM:109400	Basal cell nevus syndrome		40
HP:0009660	HP:0009660	Short phalanx of the thumb	0	RAD21 CL E G H	5885	9811	ORPHA:199	Cornelia de Lange syndrome		25
HP:0009660	HP:0009660	Short phalanx of the thumb	0	RTL1 CL E G H	388015	14665	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SALL4 CL E G H	57167	15924	ORPHA:959	Acro-renal-ocular syndrome		86
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SALL4 CL E G H	57167	15924	OMIM:147750	Ivic syndrome		86
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SETBP1 CL E G H	26040	15573	OMIM:269150	Schinzel-Giedion midface-retraction syndrome		143
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SETBP1 CL E G H	26040	15573	ORPHA:798	Schinzel-Giedion syndrome		143
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SMC1A CL E G H	8243	11111	ORPHA:199	Cornelia de Lange syndrome		135
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SMC3 CL E G H	9126	2468	ORPHA:199	Cornelia de Lange syndrome		91
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SOX9 CL E G H	6662	11204	OMIM:114290	Campomelic dysplasia		109
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SRCAP CL E G H	10847	16974	OMIM:136140	Floating-Harbor syndrome		138
HP:0009660	HP:0009660	Short phalanx of the thumb	0	SUFU CL E G H	51684	16466	OMIM:109400	Basal cell nevus syndrome		124
HP:0009660	HP:0009660	Short phalanx of the thumb	0	VPS35L CL E G H	57020	24641	OMIM:619135	RITSCHER-SCHINZEL SYNDROME 3; RTSC3
HP:0009660	HP:0010034	Short 1st metacarpal	1	ACVR1 CL E G H	90	171	OMIM:135100	Fibrodysplasia ossificans progressiva	.	49
HP:0009660	HP:0010034	Short 1st metacarpal	1	BMPR1B CL E G H	658	1077	OMIM:609441	Acromesomelic dysplasia, Demirhan type		90
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	BMPR1B CL E G H	658	1077	OMIM:616849	BRACHYDACTYLY, TYPE A1, D; BDA1D		90
HP:0009660	HP:0009638	Short proximal phalanx of thumb	1	BMPR1B CL E G H	658	1077	OMIM:616849	BRACHYDACTYLY, TYPE A1, D; BDA1D		90
HP:0009660	HP:0010034	Short 1st metacarpal	1	BRD4 CL E G H	23476	13575	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent
HP:0009660	HP:0010034	Short 1st metacarpal	1	CANT1 CL E G H	124583	19721	OMIM:251450	Desbuquois dysplasia 1	.	85
HP:0009660	HP:0010034	Short 1st metacarpal	1	DLK1 CL E G H	8788	2907	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional	1
HP:0009660	HP:0010034	Short 1st metacarpal	1	FANCI CL E G H	55215	25568	OMIM:609053	Fanconi anemia, complementation group I	.	157
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	FLNA CL E G H	2316	3754	ORPHA:1826	Frontometaphyseal dysplasia	HP:0040282 - Frequent	493
HP:0009660	HP:0010034	Short 1st metacarpal	1	FZD2 CL E G H	2535	4040	ORPHA:93328	Autosomal dominant omodysplasia	HP:0040281 - Very frequent
HP:0009660	HP:0010034	Short 1st metacarpal	1	FZD2 CL E G H	2535	4040	OMIM:164745	OMODYSPLASIA	.
HP:0009660	HP:0010034	Short 1st metacarpal	1	GDF5 CL E G H	8200	4220	ORPHA:63442	Angel-shaped phalango-epiphyseal dysplasia	HP:0040281 - Very frequent	52
HP:0009660	HP:0010034	Short 1st metacarpal	1	GDF5 CL E G H	8200	4220	OMIM:113100	Brachydactyly, type C	HP:0040282 - Frequent	52
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	GNAS CL E G H	2778	4392	ORPHA:79445	Pseudopseudohypoparathyroidism	HP:0040283 - Occasional	101
HP:0009660	HP:0010034	Short 1st metacarpal	1	HDAC8 CL E G H	55869	13315	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent	37
HP:0009660	HP:0010034	Short 1st metacarpal	1	HOXA13 CL E G H	3209	5102	ORPHA:2438	Hand-foot-genital syndrome	HP:0040281 - Very frequent	11
HP:0009660	HP:0010034	Short 1st metacarpal	1	HOXA13 CL E G H	3209	5102	OMIM:140000	Hand-Foot-Genital syndrome	.	11
HP:0009660	HP:0009638	Short proximal phalanx of thumb	1	IHH CL E G H	3549	5956	OMIM:607778	Acrocapitofemoral dysplasia		44
HP:0009660	HP:0009638	Short proximal phalanx of thumb	1	IHH CL E G H	3549	5956	OMIM:112500	Brachydactyly, type A1		44
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	KNSTRN CL E G H	90417	30767	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	1
HP:0009660	HP:0010034	Short 1st metacarpal	1	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	MAP3K7 CL E G H	6885	6859	ORPHA:1826	Frontometaphyseal dysplasia	HP:0040282 - Frequent	11
HP:0009660	HP:0010034	Short 1st metacarpal	1	MEG3 CL E G H	55384	14575	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional	1
HP:0009660	HP:0010034	Short 1st metacarpal	1	NIPBL CL E G H	25836	28862	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent	494
HP:0009660	HP:0010034	Short 1st metacarpal	1	NOG CL E G H	9241	7866	OMIM:611377	Brachydactyly, type B2		22
HP:0009660	HP:0010034	Short 1st metacarpal	1	NOG CL E G H	9241	7866	OMIM:186570	Tarsal-Carpal coalition syndrome		22
HP:0009660	HP:0010034	Short 1st metacarpal	1	PCNT CL E G H	5116	16068	OMIM:210720	Microcephalic osteodysplastic primordial dwarfism, type II	.	531
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	PIK3CD CL E G H	5293	8977	ORPHA:221139	Combined immunodeficiency with faciooculoskeletal anomalies	HP:0040282 - Frequent	9
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	PTCH1 CL E G H	5727	9585	OMIM:109400	Basal cell nevus syndrome	.	665
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	PTCH2 CL E G H	8643	9586	OMIM:109400	Basal cell nevus syndrome	.	40
HP:0009660	HP:0010034	Short 1st metacarpal	1	RAD21 CL E G H	5885	9811	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent	25
HP:0009660	HP:0010034	Short 1st metacarpal	1	RTL1 CL E G H	388015	14665	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	SALL4 CL E G H	57167	15924	ORPHA:959	Acro-renal-ocular syndrome	HP:0040281 - Very frequent	86
HP:0009660	HP:0010034	Short 1st metacarpal	1	SALL4 CL E G H	57167	15924	OMIM:147750	Ivic syndrome	.	86
HP:0009660	HP:0010034	Short 1st metacarpal	1	SETBP1 CL E G H	26040	15573	OMIM:269150	Schinzel-Giedion midface-retraction syndrome	.	143
HP:0009660	HP:0010034	Short 1st metacarpal	1	SETBP1 CL E G H	26040	15573	ORPHA:798	Schinzel-Giedion syndrome	HP:0040283 - Occasional	143
HP:0009660	HP:0010034	Short 1st metacarpal	1	SMC1A CL E G H	8243	11111	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent	135
HP:0009660	HP:0010034	Short 1st metacarpal	1	SMC3 CL E G H	9126	2468	ORPHA:199	Cornelia de Lange syndrome	HP:0040281 - Very frequent	91
HP:0009660	HP:0010034	Short 1st metacarpal	1	SOX9 CL E G H	6662	11204	OMIM:114290	Campomelic dysplasia		109
HP:0009660	HP:0010034	Short 1st metacarpal	1	SRCAP CL E G H	10847	16974	OMIM:136140	Floating-Harbor syndrome		138
HP:0009660	HP:0009650	Short distal phalanx of the thumb	1	SUFU CL E G H	51684	16466	OMIM:109400	Basal cell nevus syndrome	.	124
HP:0009660	HP:0010034	Short 1st metacarpal	1	VPS35L CL E G H	57020	24641	OMIM:619135	RITSCHER-SCHINZEL SYNDROME 3; RTSC3

Genes (34) :ACVR1 BMPR1B BRD4 CANT1 DLK1 FANCI FLNA FZD2 GDF5 GNAS HDAC8 HOXA13 IHH KCNH1 KNSTRN LAMA5 MAP3K7 MEG3 NIPBL NOG PCNT PIK3CD PTCH1 PTCH2 RAD21 RTL1 SALL4 SETBP1 SMC1A SMC3 SOX9 SRCAP SUFU VPS35L

Diseases (31) :OMIM:135100 OMIM:609441 OMIM:616849 ORPHA:199 OMIM:251450 ORPHA:96334 OMIM:609053 ORPHA:1826 ORPHA:93328 OMIM:164745 ORPHA:63442 OMIM:113100 ORPHA:79445 OMIM:140000 ORPHA:2438 OMIM:607778 OMIM:112500 ORPHA:420561 ORPHA:221139 OMIM:620076 OMIM:611377 OMIM:186570 OMIM:210720 OMIM:109400 ORPHA:959 OMIM:147750 OMIM:269150 ORPHA:798 OMIM:114290 OMIM:136140 OMIM:619135

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