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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

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

Disease Browser
Parent Node: alpha-Thalassemia (D017085)
Parent Node: Mental Retardation, X-Linked (D038901)
..Starting node ..ATR-X syndrome (C538258)
Child Nodes:
Sister Nodes:
..Abidi X-linked mental retardation syndrome (C535556)
..Adrenoleukodystrophy (D000326) 4
..Aldred syndrome (C537046)
..Allan-Herndon-Dudley syndrome (C537047)
..Arena syndrome (C537428)
..Armfield X-Linked Mental Retardation Syndrome (C564551)
..Atkin syndrome (C538195)
..ATR-X syndrome (C538258)
..Borjeson-Forssman-Lehmann syndrome (C536575)
..Brooks-Wisniewski-Brown Syndrome (C563154)
..Chromosome Xp11.3 Deletion Syndrome (C564481)
..CK SYNDROME (OMIM:300831)
..Clark-Baraitser syndrome (C536208)
..Classical Lissencephalies and Subcortical Band Heterotopias (D054221) 5
..Coffin-Lowry Syndrome (D038921)
..Cowchock syndrome (C536450)
..Creatine deficiency, X-linked (C535598)
..Encephalopathy, Neonatal Severe, Due To Mecp2 Mutations (C566878)
..Faciogenital Dysplasia with Attention Deficit-Hyperactivity Disorder (C564427)
..Fragile X Syndrome (D005600) 3
..Glycogen Storage Disease Type IIb (D052120)
..Lesch-Nyhan Syndrome (D007926) 1
..Lubs X-linked mental retardation syndrome (C537723)
..Lujan Fryns syndrome (C537724)
..MEHMO syndrome (C537451)
..Menkes Kinky Hair Syndrome (D007706) 1
..Mental Retardation And Microcephaly With Pontine And Cerebellar Hypoplasia (C567466)
..Mental Retardation with Psychosis, Pyramidal Signs, and Macroorchidism (C564724)
..Mental retardation X-linked syndromic 7 (C537449)
..Mental retardation X-linked, South African type (C537450)
..Mental Retardation, X-Linked 1 (C567906)
..Mental retardation, X-linked 14 (C537454)
..Mental Retardation, X-Linked 16 (C563139)
..Mental Retardation, X-Linked 17 (C563140)
..Mental Retardation, X-Linked 19 (C563141)
..Mental Retardation, X-Linked 2 (C563135)
..Mental Retardation, X-Linked 20 (C563142)
..MENTAL RETARDATION, X-LINKED 21 (OMIM:300143)
..Mental Retardation, X-Linked 23 (C563144)
..Mental Retardation, X-Linked 3 (C563136)
..Mental Retardation, X-Linked 30 (C563146)
..Mental Retardation, X-Linked 31 (C563147)
..Mental Retardation, X-Linked 34 (C563148)
..Mental Retardation, X-Linked 42 (C564524)
..Mental Retardation, X-Linked 45 (C564503)
..Mental Retardation, X-Linked 46 (C564513)
..Mental Retardation, X-Linked 47 (C563151)
..MENTAL RETARDATION, X-LINKED 49 (OMIM:300114)
..Mental Retardation, X-Linked 50 (C564713)
..Mental Retardation, X-Linked 52 (C564502)
..Mental Retardation, X-Linked 53 (C564533)
..Mental Retardation, X-Linked 58 (C564566)
..Mental Retardation, X-Linked 59 (C564470)
..Mental Retardation, X-Linked 63 (C564522)
..Mental Retardation, X-Linked 72 (C564547)
..Mental Retardation, X-Linked 73 (C564528)
..Mental Retardation, X-Linked 77 (C564511)
..Mental Retardation, X-Linked 78 (C564489)
..Mental Retardation, X-Linked 79 (C566876)
..Mental Retardation, X-Linked 81 (C564515)
..Mental Retardation, X-Linked 82 (C564496)
..Mental Retardation, X-Linked 84 (C564501)
..Mental Retardation, X-Linked 89 (C564036)
..Mental Retardation, X-Linked 9 (C563137)
..Mental Retardation, X-Linked 91 (C564482)
..Mental Retardation, X-Linked 92 (C564483)
..Mental Retardation, X-Linked 93 (C567066)
..Mental Retardation, X-Linked 94 (C567479)
..Mental Retardation, X-Linked 95 (C567470)
..MENTAL RETARDATION, X-LINKED 96 (OMIM:300802)
..Mental Retardation, X-Linked Nonsyndromic (C564490)
..Mental Retardation, X-Linked, Syndromic 10 (C564560)
..Mental Retardation, X-Linked, Syndromic 13 (C566875)
..Mental Retardation, X-Linked, Syndromic 14 (C567063)
..Mental retardation, X-linked, syndromic 5 (C535773)
..Mental Retardation, X-Linked, Syndromic 9 (C567474)
..Mental Retardation, X-Linked, Syndromic, Jarid1c-Related (C564494)
..MENTAL RETARDATION, X-LINKED, SYNDROMIC, RAYMOND TYPE (OMIM:300799)
..Mental Retardation, X-Linked, Syndromic, Ube2a-Related (C564069)
..Mental Retardation, X-Linked, Syp-Related (C567584)
..Mental Retardation, X-Linked, With Brachydactyly And Macroglossia (C567069)
..Mental retardation, X-linked, with cerebellar hypoplasia and distinctive facial appearance (C537456)
..Mental Retardation, X-Linked, with Epilepsy (C564516)
..Mental Retardation, X-Linked, with Isolated Growth Hormone Deficiency (C564712)
..Mental Retardation, X-Linked, With Or Without Seizures, Arx-Related (C563150)
..Mental Retardation, X-Linked, with Short Stature (C564527)
..MENTAL RETARDATION, X-LINKED, WITH SHORT STATURE, HYPOGONADISM, AND ABNORMAL GAIT (OMIM:300354)
..Mental Retardation, X-Linked, With Spasticity (C566877)
..Mental retardation-hypotonic facies syndrome, x-linked, 1 (C537457)
..Microphthalmia, Syndromic 4 (C564457)
..Miles-Carpenter x-linked mental retardation syndrome (C537472)
..Mucopolysaccharidosis II (D016532)
..Opitz-Kaveggia syndrome (C537923)
..Orofaciodigital syndrome, Shashi type (C537135)
..Partington X-linked mental retardation syndrome (C536300)
..Plagiocephaly and X-linked mental retardation (C537512)
..Ppm-X Syndrome (C580387)
..Prieto X-linked mental retardation syndrome (C535274)
..Pyruvate Dehydrogenase Complex Deficiency Disease (D015325) 4
..Renpenning syndrome 1 (C537761)
..Rett Syndrome (D015518) 5
..Roifman syndrome (C535866)
..Schimke X-linked mental retardation syndrome (C536630)
..Siderius X-linked mental retardation syndrome (C537333)
..Snyder Robinson syndrome (C536678)
..Stocco dos Santos syndrome (C537495)
..Tranebjaerg Svejgaard syndrome (C536978)
..Wilson-Turner X-linked mental retardation syndrome (C536708)
..Wittwer syndrome (C536737)
..X-linked mental retardation Gustavson type (C536759)
..X-linked mental retardation type Wittwer (C536760)
Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM, CTD

Term ID:

1050

Name:

ATR-X syndrome

Definition:

Alternative IDs:

OMIM:301040

ParentIDs:

MESH:D017085|MESH:D038901

TreeNumbers:

C10.597.606.643.455/C538258 |C15.378.071.141.150.875.100/C538258 |C15.378.420.826.100/C538258 |C16.320.070.875.100/C538258 |C16.320.322.500/C538258 |C16.320.365.826.100/C538258 |C16.320.400.525/C538258

Synonyms:

Alpha-Thalassemia-Mental Retardation Syndrome, Nondeletion Type |ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, NONDELETION TYPE |Alpha thalassemia mental retardation syndrome, non deletion type, X-linked |Alpha-Thalassemia-Mental Retardation Syndrome, Nond

Slim Mappings:

Blood disease|Genetic disease (inborn)|Nervous system disease

Reference:

MedGen: C538258
MeSH: C538258
OMIM: 301040;

Genes: ATRX;

Phenotypes

1	HP:0001423	X-linked dominant inheritance
2	HP:0001939	Abnormality of metabolism/homeostasis
3	HP:0002688	Absent frontal sinuses
4	HP:0000463	Anteverted nares
5	HP:0002059	Cerebral atrophy
6	HP:0030084	Clinodactyly
7	HP:0002019	Constipation
8	HP:0002673	Coxa valga
9	HP:0000028	Cryptorchidism
10	HP:0005280	Depressed nasal bridge
11	HP:0000286	Epicanthus
12	HP:0002020	Gastroesophageal reflux
13	HP:0001263	Global developmental delay
14	HP:0001510	Growth delay
15	HP:0002937	Hemivertebrae
16	HP:0000126	Hydronephrosis
17	HP:0000316	Hypertelorism
18	HP:0004840	Hypochromic microcytic anemia
19	HP:0000047	Hypospadias
20	HP:0008947	Infantile muscular hypotonia
21	HP:0001249	Intellectual disability
22	HP:0002751	Kyphoscoliosis
23	HP:0000369	Low-set ears
24	HP:0000158	Macroglossia
25	HP:0000272	Malar flattening
26	HP:0000252	Microcephaly
27	HP:0000054	Micropenis
28	HP:0008551	Microtia
29	HP:0011682	Perimembranous ventricular septal defect
30	HP:0003812	Phenotypic variability
31	HP:0000358	Posteriorly rotated ears
32	HP:0008897	Postnatal growth retardation
33	HP:0010808	Protruding tongue
34	HP:0009466	Radial deviation of finger
35	HP:0011907	Reduced alpha/beta synthesis ratio
36	HP:0000104	Renal agenesis
37	HP:0001250	Seizure	HP:0040282
38	HP:0000407	Sensorineural hearing impairment
39	HP:0000049	Shawl scrotum
40	HP:0003196	Short nose
41	HP:0001257	Spasticity
42	HP:0001762	Talipes equinovarus
43	HP:0001182	Tapered finger
44	HP:0000179	Thick lower lip vermilion
45	HP:0010806	U-Shaped upper lip vermilion
46	HP:0001537	Umbilical hernia
47	HP:0001629	Ventricular septal defect
48	HP:0001566	Widely-spaced maxillary central incisors

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_000489.4(ATRX):c.7366_7367delAT (p.Met2456Glufs)	546	ATRX	Likely pathogenic	797044723	RCV000177828;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76763941	76763942	NM_000489.4:c.7366_7367delAT	NP_000480.3:p.Met2456Glufs	NC_000023.10:g.76763941_76763942delAT	-	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.7162G>T (p.Glu2388Ter)	546	ATRX	Pathogenic	122445100	RCV000012495;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76776304	76776304	NM_000489.4:c.7162G>T	NP_000480.3:p.Glu2388Ter	NC_000023.10:g.76776304C>A	OMIM Allelic Variant:300032.0009	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.7156C>T (p.Arg2386Ter)	546	ATRX	Pathogenic	122445099	RCV000012494;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76776310	76776310	NM_000489.4:c.7156C>T	NP_000480.3:p.Arg2386Ter	NC_000023.10:g.76776310G>A	OMIM Allelic Variant:300032.0008	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.6718C>T (p.Leu2240Phe)	546	ATRX	not provided	199474698	RCV000144410;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76778861	76778861	NM_000489.4:c.6718C>T	NP_000480.3:p.Leu2240Phe	NC_000023.10:g.76778861G>A	-	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.6488A>G (p.Tyr2163Cys)	546	ATRX	Pathogenic	122445098	RCV000012493;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76814156	76814156	NM_000489.4:c.6488A>G	NP_000480.3:p.Tyr2163Cys	NC_000023.10:g.76814156T>C	OMIM Allelic Variant:300032.0007	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.6392G>A (p.Arg2131Gln)	546	ATRX	Pathogenic	122445101	RCV000012497; RCV000199096;	N	MedGen:C0796003,OMIM:309580,ORPHA:93972; MedGen:C1845055,OMIM:301040,ORPHA:847; MedGen:C4016452	X	76814252	76814252	NM_000489.4:c.6392G>A	NP_000480.3:p.Arg2131Gln	NC_000023.10:g.76814252C>T	OMIM Allelic Variant:300032.0011	C1845055 301040 ATR-X syndrome; C0796003 309580 Mental retardation-hypotonic facies syndrome X-linked, 1; C4016452 Mental retardation-hypotonic facies syndrome, X-linked
NM_000489.4(ATRX):c.6250T>C (p.Tyr2084His)	546	ATRX	Pathogenic	122445097	RCV000012492;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76829791	76829791	NM_000489.4:c.6250T>C	NP_000480.3:p.Tyr2084His	NC_000023.10:g.76829791A>G	OMIM Allelic Variant:300032.0006	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.6104A>T (p.Asp2035Val)	546	ATRX	Pathogenic	122445096	RCV000012491;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76849172	76849172	NM_000489.4:c.6104A>T	NP_000480.3:p.Asp2035Val	NC_000023.10:g.76849172T>A	OMIM Allelic Variant:300032.0005	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.5579A>G (p.Asn1860Ser)	546	ATRX	Benign;Pathogenic	45439799	RCV000012490; RCV000078966;	N	MedGen:C1845055,OMIM:301040,ORPHA:847; MedGen:CN169374	X	76856021	76856021	NM_000489.4:c.5579A>G	NP_000480.3:p.Asn1860Ser	NC_000023.10:g.76856021T>C	HGMD:CM950125,OMIM Allelic Variant:300032.0004	C1845055 301040 ATR-X syndrome; CN169374 not specified
NM_000489.4(ATRX):c.5225G>A (p.Arg1742Lys)	546	ATRX	Pathogenic	122445104	RCV000012502;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76875910	76875910	NM_000489.4:c.5225G>A	NP_000480.3:p.Arg1742Lys	NC_000023.10:g.76875910C>T	OMIM Allelic Variant:300032.0016	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.4950G>T (p.Lys1650Asn)	546	ATRX	Pathogenic	122445095	RCV000012489;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76889060	76889060	NM_000489.4:c.4950G>T	NP_000480.3:p.Lys1650Asn	NC_000023.10:g.76889060C>A	OMIM Allelic Variant:300032.0003	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.4862C>T (p.Thr1621Met)	546	ATRX	Pathogenic	122445106	RCV000012505;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76889148	76889148	NM_000489.4:c.4862C>T	NP_000480.3:p.Thr1621Met	NC_000023.10:g.76889148G>A	OMIM Allelic Variant:300032.0019	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.4840T>C (p.Cys1614Arg)	546	ATRX	Pathogenic	122445094	RCV000012488;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76889170	76889170	NM_000489.4:c.4840T>C	NP_000480.3:p.Cys1614Arg	NC_000023.10:g.76889170A>G	OMIM Allelic Variant:300032.0002	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.4826A>G (p.His1609Arg)	546	ATRX	Pathogenic	122445093	RCV000012487;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76889184	76889184	NM_000489.4:c.4826A>G	NP_000480.3:p.His1609Arg	NC_000023.10:g.76889184T>C	OMIM Allelic Variant:300032.0001	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.4626_4631delTGAAGA (p.Asp1542_Glu1543del)	546	ATRX	Likely pathogenic	797045406	RCV000193225;	N	MedGen:C1845055,OMIM:301040,ORPHA:847	X	76891474	76891479	NM_000489.4:c.4626_4631delTGAAGA	NP_000480.3:p.Asp1542_Glu1543del	NC_000023.10:g.76891474_76891479delTCTTCA	-	C1845055 301040 ATR-X syndrome
NM_000489.4(ATRX):c.736C>T (p.Arg246Cys)	546	ATRX	Pathogenic	122445105	RCV000012501; RCV000078972; RCV000190796;	N	MedGen:C0950123; MedGen:C1845055,OMIM:301040,ORPHA:847; MedGen:CN221809	X	76940012	76940012	NM_000489.4:c.736C>T	NP_000480.3:p.Arg246Cys	NC_000023.10:g.76940012G>A	OMIM Allelic Variant:300032.0015,OMIM Allelic Variant:300032.0018	C1845055 301040 ATR-X syndrome; C0950123 Inborn genetic diseases; CN221809 not provided
NM_000489.4(ATRX):c.568C>G (p.Pro190Ala)	546	ATRX	Likely pathogenic;Pathogenic	122445103	RCV000012500; RCV000197579;	N	MedGen:C0796003,OMIM:309580,ORPHA:93972; MedGen:C1845055,OMIM:301040,ORPHA:847	X	76944337	76944337	NM_000489.4:c.568C>G	NP_000480.3:p.Pro190Ala	NC_000023.10:g.76944337G>C	OMIM Allelic Variant:300032.0014	C1845055 301040 ATR-X syndrome; C0796003 309580 Mental retardation-hypotonic facies syndrome X-linked, 1
NM_000489.4(ATRX):c.109C>T (p.Arg37Ter)	546	ATRX	Pathogenic	122445108	RCV000148028; RCV000012508;	N	MedGen:C1845055,OMIM:301040,ORPHA:847; MedGen:C4016452	X	76972632	76972632	NM_000489.4:c.109C>T	NP_000480.3:p.Arg37Ter	NC_000023.10:g.76972632G>A	OMIM Allelic Variant:300032.0022	C1845055 301040 ATR-X syndrome; C4016452 Mental retardation-hypotonic facies syndrome, X-linked