MSeqDR Mitochondrial disease browser phenotype pathogenic gene and mutation portal

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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

MSeqDR Mitochondrial Disease Portal

*:HP: HPO terms, UMDF: 1= Disease, ND: NAMDC terms.
Most Studied CPEO, Complex I Deficiency, COXPD1, Leigh, LHON, MELAS, MERRF, Myopathy, SANDO

Disease Browser
Parent Node: Mental Retardation, X-Linked (D038901)
Parent Node: Sex Chromosome Disorders (D025064)
..Starting node ..Fragile X Syndrome (D005600)
Child Nodes:
........Fragile X Tremor Ataxia Syndrome (C564105)
........Saul Wilkes Stevenson syndrome (C536617)
Sister Nodes:
..47, XYY syndrome (C535317)
..49,XXXXX syndrome (C535319)
..Chromosome Xq duplication syndrome (C536732)
..Chromosome Xq28 Duplication Syndrome (C567580)
..Fragile X Syndrome (D005600) 3
..Orofaciodigital Syndromes (D009958) 14
..Sex Chromosome Disorders of Sex Development (D058533) 8
Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM,ClinVar, CTD

Term ID:

4857

Name:

Fragile X Syndrome

Definition:

A condition characterized genotypically by mutation of the distal end of the long arm of the X chromosome (at gene loci FRAXA or FRAXE) and phenotypically by cognitive impairment, hyperactivity, SEIZURES, language delay, and enlargement of the ears, head, and testes. INTELLECTUAL DISABILITY occurs in nearly all males and roughly 50% of females with the full mutation of FRAXA. (From Menkes, Textbook of Child Neurology, 5th ed, p226)

Alternative IDs:

DO:DOID:14261|OMIM:300624|OMIM:309548

ParentIDs:

MESH:D025064|MESH:D038901

TreeNumbers:

C10.597.606.360.455.500 |C16.131.260.830.300 |C16.320.180.830.300 |C16.320.322.500.500 |C16.320.400.525.500

Synonyms:

Slim Mappings:

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

Reference:

MedGen: D005600
MeSH: D005600
OMIM: 300624;
MSeqDR :
Genes: AFF2; FMR1;

Phenotypes

1	HP:0001423	X-linked dominant inheritance
2	HP:0002457	Abnormal head movements
3	HP:0000717	Autism NAMDC: Autism
4	HP:0000280	Coarse facial features
5	HP:0008640	Congenital macroorchidism
6	HP:0003564	Folate-dependent fragile site at Xq28
7	HP:0000752	Hyperactivity
8	HP:0003829	Incomplete penetrance
9	HP:0002342	Intellectual disability, moderate	HP:0040282
10	HP:0001388	Joint laxity
11	HP:0002003	Large forehead
12	HP:0000276	Long face
13	HP:0000256	Macrocephaly
14	HP:0002050	Macroorchidism, postpubertal
15	HP:0000400	Macrotia
16	HP:0000303	Mandibular prognathia
17	HP:0001634	Mitral valve prolapse
18	HP:0000767	Pectus excavatum
19	HP:0007165	Periventricular gray matter heterotopia
20	HP:0001763	Pes planus
21	HP:0000817	Poor eye contact
22	HP:0002650	Scoliosis
23	HP:0001250	Seizures NAMDC: Seizures

Disease Causing ClinVar Variants

Variation_Name	GeneID	GeneSymbol	ClinicalSignificance	dbSNP	RCVaccession	TestedInGTR	PhenotypeIDs	Chromosome	Start	Stop	HGVS_g	OtherIDs	Disease_ClinVar
NC_000006.11:g.146735206_147036914del301709	-1	ADGB;ADGB-DT;GRM1;LOC114004398;LOC129997388;RAB32	Pathogenic	-1	RCV000234921;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	6	146735206	147036914		-	C0016667 300624 Fragile X syndrome;
NM_002024.6(FMR1):c.-129CGG[201]	2332	FMR1	Pathogenic	193922936	RCV000162201;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	146993570	146993572	NC_000023.10:g.146993569CGG[201]	-	C0016667 300624 Fragile X syndrome;
NM_002024.6(FMR1):c.-128GGC[200_?]	2332	FMR1	Pathogenic	-1	RCV000761552;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	146993570	146993570		-
NC_000023.10:g.146993570GGC[(?_45)]	2332	FMR1	Benign	-1	RCV001249605;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	146993570	146993570	-1	-
NM_002024.6(FMR1):c.-98GGC[11]	2332	FMR1	Benign	782036637	RCV001678618\|RCV001827581;	N	MedGen:C3661900\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	146993599	146993600	146993599	-
NM_002024.6(FMR1):c.18G>T (p.Val6=)	2332	FMR1	Benign/Likely benign	111485627	RCV000727572\|RCV002312464\|RCV002485801;	N	MedGen:CN169374\|MeSH:D030342,MedGen:C0950123\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908; MONDO:MONDO:0010706,MedGen:C4552079,OMIM:311360; MONDO:MONDO:0010382,MedGen:C1839780,OMIM:300623, Orphanet:93256	X	146993715	146993715	NC_000023.10:g.146993715G>T	-
NM_002024.6(FMR1):c.52-1_52delinsTA	2332	FMR1	Pathogenic	1557176576	RCV000010650;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147003450	147003451	NC_000023.10:g.147003450_147003451delinsTA	ClinGen:CA658799869,OMIM:309550.0003	C0016667 300624 Fragile X syndrome;
NM_002024.6(FMR1):c.80C>A (p.Ser27Ter)	2332	FMR1	Pathogenic	1569545382	RCV000022880;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147003479	147003479	NC_000023.10:g.147003479C>A	OMIM:309550.0005
NM_002024.6(FMR1):c.357A>C (p.Lys119Asn)	2332	FMR1	Likely benign	201580891	RCV000990957;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147010263	147010263	X:g.147010263A>C	-
NM_002024.6(FMR1):c.373del (p.Thr125fs)	2332	FMR1	Pathogenic	1569545562	RCV000010649;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147010279	147010279	NC_000023.10:g.147010279del	OMIM:309550.0002
NM_002024.6(FMR1):c.413G>A (p.Arg138Gln)	2332	FMR1	Uncertain significance	200163413	RCV002275611;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147010319	147010319	147010319	-
NM_002024.6(FMR1):c.414G>A (p.Arg138=)	2332	FMR1	Benign	25707	RCV000079966\|RCV001276519\|RCV001668194\|RCV002311599\|RCV002498405;	N	MedGen:CN169374\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908\|MedGen:C3661900\|MeSH:D030342,MedGen:C0950123\|MONDO:MONDO:0010706,MedGen:C4552079,OMIM:311360; MONDO:MONDO:0010382,MedGen:C1839780,OMIM:300623, Orphanet:93256; MOND	X	147010320	147010320	X:g.147010320G>A	ClinGen:CA147545	CN169374 not specified;
NM_002024.6(FMR1):c.433G>T (p.Ala145Ser)	2332	FMR1	Benign	29281	RCV000117089\|RCV001276520\|RCV002312108\|RCV002477289;	N	MedGen:CN169374\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908\|MeSH:D030342,MedGen:C0950123\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908; MONDO:MONDO:0010706,MedGen:C4552079,OMIM:311360; MONDO:	X	147011480	147011480	X:g.147011480G>T	ClinGen:CA152897,UniProtKB:Q06787#VAR_029278	CN169374 not specified;
NM_002024.6(FMR1):c.786T>G (p.Phe262Leu)	2332	FMR1	Uncertain significance	2124521147	RCV002222282;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147014099	147014099	147014099	-
NM_002024.6(FMR1):c.818A>G (p.Lys273Arg)	2332	FMR1	Benign/Likely benign	139029212	RCV000513003\|RCV001195728\|RCV002527421;	N	MedGen:C3661900\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908\|MeSH:D030342,MedGen:C0950123	X	147014220	147014220	X:g.147014220A>G	ClinGen:CA10536229	CN517202 not provided;
NM_002024.6(FMR1):c.911T>A (p.Ile304Asn)	2332	FMR1	Pathogenic	121434622	RCV000010648;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147018053	147018053	X:g.147018053T>A	ClinGen:CA254953,UniProtKB:Q06787#VAR_005234,OMIM:309550.0001	C0016667 300624 Fragile X syndrome;
NM_002024.6(FMR1):c.990+14C>T	2332	FMR1	Benign	25714	RCV000079968\|RCV001682769\|RCV001826716;	N	MedGen:CN169374\|MedGen:C3661900\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147018146	147018146	X:g.147018146C>T	ClinGen:CA147547	CN169374 not specified;
NM_002024.6(FMR1):c.1184G>A (p.Trp395Ter)	2332	FMR1	Likely pathogenic	2043856428	RCV001328911;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147019676	147019676	147019676	-
NM_002024.6(FMR1):c.1268_1269del (p.Tyr423fs)	2332	FMR1	Likely pathogenic	-1	RCV002287600;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147022173	147022174	147022172	-
NM_002024.6(FMR1):c.1282G>C (p.Asp428His)	2332	FMR1	Uncertain significance	2044064790	RCV001328912;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147024657	147024657	147024657	-
NM_002024.6(FMR1):c.1325G>A (p.Arg442Gln)	2332	FMR1	Conflicting interpretations of pathogenicity	-1	RCV002465415\|RCV003149035\|RCV003317610;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908\|MedGen:CN517202\|MedGen:CN169374	X	147024700	147024700	NC_000023.10:g.147024700G>A	-
NM_002024.6(FMR1):c.1572C>T (p.Ser524=)	2332	FMR1	Benign/Likely benign	143889976	RCV000193183\|RCV001276521\|RCV001573098\|RCV002317683;	N	MedGen:CN169374\|MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908\|MedGen:C3661900\|MeSH:D030342,MedGen:C0950123	X	147026489	147026489	X:g.147026489C>T	ClinGen:CA206490	CN169374 not specified;
NM_002024.6(FMR1):c.1691G>A (p.Arg564His)	2332	FMR1	Uncertain significance	-1	RCV003329098;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147027090	147027090		-
NM_002024.6(FMR1):c.1831C>T (p.Arg611Cys)	2332	FMR1	Uncertain significance	961588789	RCV002272691;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147030296	147030296	147030296	-
NM_002024.6(FMR1):c.*746T>C	2332	FMR1	Benign	183130936	RCV000990958;	N	MONDO:MONDO:0010383,MedGen:C0016667,OMIM:300624, Orphanet:449291, Orphanet:908	X	147031110	147031110	X:g.147031110T>C	-

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