Disease browser and phenotype portal

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

Hearing Loss Disease Portal

Switch to table view
Most Common: Hearing Loss (D034381), Deafness (D003638), Sensorineural HL (D006319), Waardenburg Syndrome, Usher Syndromes

Disease Browser
Parent Node: Holoprosencephaly (D016142)
Parent Node: Hypopituitarism (D007018)
Parent Node: Polydactyly (D017689)
..Starting node ..Holoprosencephaly 9 (C563659)
Child Nodes:
Sister Nodes:
..Absence of tibia with polydactyly (C535564)
..Biemond Syndrome II (C565902)
..Biemond syndrome type 2 (C535439)
..Brachyphalangy, polydactyly, and tibial aplasia/hypoplasia (C537100)
..Cortical Blindness, Retardation, and Postaxial Polydactyly (C565674)
..Crossed Polydactyly, Type I (C566783)
..Dandy Walker malformation postaxial polydactyly (C535771)
..Desbuquois syndrome (C535943)
..Ectodermal dysplasia alopecia preaxial polydactyly (C538016)
..Ectodermal Dysplasia Syndrome with Distinctive Facial Appearance and Preaxial Polydactyly of Feet (C565067)
..Garret Tripp syndrome (C535646)
..Hirschsprung disease polydactyly heart disease (C538120)
..Hirschsprung Disease with Heart Defects, Laryngeal Anomalies, and Preaxial Polydactyly (C565817)
..Hirschsprung Disease with Polydactyly, Renal Agenesis, and Deafness (C565518)
..Hirschsprung Disease with Ulnar Polydactyly, Polysyndactyly of Big Toes, and Ventricular Septal Defect (C565517)
..Holoprosencephaly 9 (C563659)
..Hydrolethalus Syndrome 1 (C565504)
..Kozlowski-Krajewska syndrome (C537615)
..Laurence Prosser Rocker syndrome (C537882)
..Liver Fibrocystic Disease and Polydactyly (C565272)
..Maroteaux Fonfria syndrome (C536023)
..McKusick Kaufman syndrome (C538159)
..Meckel Syndrome, Type 4 (C567003)
..Meckel-Like Cerebrorenodigital Syndrome (C567004)
..Megalanecephaly Polymicrogyria-Polydactyly Hydrocephalus Syndrome (C566381)
..Mexican Cardiomelic Dysplasia (C563087)
..Oliver Syndrome (C564931)
..Pallister-Hall Syndrome (D054975)
..Pfeiffer Mayer syndrome (C537888)
..Polydactyly myopia syndrome (C536331)
..Polydactyly preaxial type 1 (C536332)
..Polydactyly, Postaxial (C562429)
..Polydactyly, Postaxial, Type A2 (C566585)
..Polydactyly, Postaxial, Type A3 (C564590)
..Polydactyly, Postaxial, Type A4 (C563909)
..Polydactyly, Postaxial, with Dental and Vertebral Anomalies (C564880)
..Polydactyly, preaxial 4 (C536333)
..POLYDACTYLY, PREAXIAL II (OMIM:174500)
..Polydactyly, Preaxial III (C566784)
..Polysyndactyly, Crossed (C566773)
..Preaxial deficiency, postaxial polydactyly and hypospadias (C538278)
..Preaxial Hallucal Polydactyly (C566632)
..Pseudotrisomy 13 syndrome (C535829)
..Santos Mateus Leal syndrome (C537235)
..Santos Syndrome (C567819)
..Scalp defects postaxial polydactyly (C536622)
..Short Rib-Polydactyly Syndrome (D012779) 3
..SHORT-RIB THORACIC DYSPLASIA 3 WITH OR WITHOUT POLYDACTYLY (OMIM:613091)
..Syndactyly, Type IV (C566092)
..Syndactyly-Polydactyly-Earlobe Syndrome (C566091)
..Synpolydactyly 2 (C564278)
..Synpolydactyly 3 (C565216)
..Synpolydactyly With Foot Anomalies (C566095)
..Thai Symphalangism Syndrome (C564303)
..Tibia absent polydactyly arachnoid cyst (C536918)
..Tibia, Absence or Hypoplasia of, with Polydactyly, Retrocerebellar Arachnoid Cyst, and Other Anomalies (C563403)
..Tibia, Hypoplasia of, with Polydactyly (C566046)
..Ulnar Ray Dysgenesis with Postaxial Polydactyly and Renal Cystic Dysplasia (C565783)
..Urioste Martinez-Frias syndrome (C536478)
Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM, CTD

Term ID:

5248

Name:

Holoprosencephaly 9

Definition:

Alternative IDs:

OMIM:610829

ParentIDs:

MESH:D007018|MESH:D016142|MESH:D017689

TreeNumbers:

C05.660.207.410/C563659 |C05.660.585.600/C563659 |C10.228.140.617.738.300/C563659 |C10.500.034.875/C563659 |C16.131.077.410/C563659 |C16.131.260.380/C563659 |C16.131.621.207.410/C563659 |C16.131.621.585.600/C563659 |C16.131.666.034.875/C563659 |C16.320.180.380/C5

Synonyms:

HOLOPROSENCEPHALY WITH MICROPHTHALMIA AND FIRST BRANCHIAL ARCH ANOMALIES |HPE9 |Pituitary Anomalies with Holoprosencephaly-Like Features

Slim Mappings:

Congenital abnormality|Endocrine system disease|Genetic disease (inborn)|Musculoskeletal disease|Nervous system disease

Reference:

MedGen: C563659
MeSH: C563659
OMIM: 610829;

Genes: GLI2;

Phenotypes

1	HP:0000006	Autosomal dominant inheritance
2	HP:0002536	Abnormal cortical gyration
3	HP:0006485	Agenesis of incisor
4	HP:0000528	Anophthalmia
5	HP:0010626	Anterior pituitary agenesis
6	HP:0010627	Anterior pituitary hypoplasia
7	HP:0002744	Bilateral cleft lip and palate
8	HP:0000028	Cryptorchidism
9	HP:0000824	Decreased response to growth hormone stimulation test
10	HP:0000689	Dental malocclusion
11	HP:0005280	Depressed nasal bridge
12	HP:0001263	Global developmental delay
13	HP:0001360	Holoprosencephaly
14	HP:0000238	Hydrocephalus
15	HP:0000327	Hypoplasia of the maxilla
16	HP:0010650	Hypoplasia of the premaxilla
17	HP:0000601	Hypotelorism
18	HP:0003829	Incomplete penetrance
19	HP:0000400	Macrotia
20	HP:0000272	Malar flattening
21	HP:0000252	Microcephaly
22	HP:0000054	Micropenis
23	HP:0000568	Microphthalmia
24	HP:0011800	Midface retrusion
25	HP:0000609	Optic nerve hypoplasia
26	HP:0000871	Panhypopituitarism
27	HP:0001338	Partial agenesis of the corpus callosum
28	HP:0001162	Postaxial hand polydactyly
29	HP:0000395	Prominent antihelix
30	HP:0001250	Seizure
31	HP:0010290	Short hard palate
32	HP:0000322	Short philtrum
33	HP:0004322	Short stature	HP:0040283
34	HP:0009932	Single naris
35	HP:0006315	Solitary median maxillary central incisor
36	HP:0003745	Sporadic
37	HP:0011272	Underdeveloped tragus
38	HP:0003828	Variable expressivity

Disease Causing ClinVar Variants

Variation_Name	GeneID	GeneSymbol	ClinicalSignificance	dbSNP	RCVaccession	TestedInGTR	PhenotypeIDs	Chromosome	Start	Stop	HGVS_c	HGVS_p	HGVS_g	OtherIDs	Disease_ClinVar
NM_005270.4(GLI2):c.864_865delCC (p.His289Profs)	2736	GLI2	Pathogenic	398122882	RCV000030729;	N	MedGen:C1835819,OMIM:610829	2	121727987	121727988	NM_005270.4:c.864_865delCC	NP_005261.2:p.His289Profs	NC_000002.11:g.121727987_121727988delCC	OMIM Allelic Variant:165230.0005	C1835819 610829 Holoprosencephaly 9
NM_005270.4(GLI2):c.1323G>A (p.Trp441Ter)	2736	GLI2	Pathogenic	121917707	RCV000014847;	N	MedGen:C1835819,OMIM:610829	2	121732640	121732640	NM_005270.4:c.1323G>A	NP_005261.2:p.Trp441Ter	NC_000002.11:g.121732640G>A	OMIM Allelic Variant:165230.0002	C1835819 610829 Holoprosencephaly 9
NM_005270.4(GLI2):c.1435C>G (p.Arg479Gly)	2736	GLI2	Pathogenic	121917708	RCV000014848;	N	MedGen:C1835819,OMIM:610829	2	121736076	121736076	NM_005270.4:c.1435C>G	NP_005261.2:p.Arg479Gly	NC_000002.11:g.121736076C>G	OMIM Allelic Variant:165230.0003	C1835819 610829 Holoprosencephaly 9
NM_005270.4(GLI2):c.1885G>A (p.Glu629Lys)	2736	GLI2	Pathogenic	387907277	RCV000030730;	N	MedGen:C1835819,OMIM:610829	2	121742248	121742248	NM_005270.4:c.1885G>A	NP_005261.2:p.Glu629Lys	NC_000002.11:g.121742248G>A	OMIM Allelic Variant:165230.0006	C1835819 610829 Holoprosencephaly 9
NM_005270.4(GLI2):c.4558G>A (p.Asp1520Asn)	2736	GLI2	Benign;Pathogenic	114814747	RCV000030731; RCV000174553;	N	MedGen:C1835819,OMIM:610829; MedGen:CN169374	2	121748048	121748048	NM_005270.4:c.4558G>A	NP_005261.2:p.Asp1520Asn	NC_000002.11:g.121748048G>A	OMIM Allelic Variant:165230.0007	C1835819 610829 Holoprosencephaly 9; CN169374 not specified
NM_005270.4(GLI2):c.4663T>C (p.Ser1555Pro)	2736	GLI2	Benign;Pathogenic	144372453	RCV000030728; RCV000174544;	N	MedGen:C1835819,OMIM:610829; MedGen:CN169374	2	121748153	121748153	NM_005270.4:c.4663T>C	NP_005261.2:p.Ser1555Pro	NC_000002.11:g.121748153T>C	OMIM Allelic Variant:165230.0004	C1835819 610829 Holoprosencephaly 9; CN169374 not specified