MSeqDR Mitochondrial disease browser phenotype pathogenic gene and mutation portal

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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

MSeqDR Mitochondrial Disease Portal

*:HP: HPO terms, ND: NAMDC terms.
Most Studied CPEO, Complex I Deficiency, COXPD1, Leigh, LHON, MELAS, MERRF, NARP, SANDO

Disease Browser
Parent Node: congenital disorder of glycosylation type II (MONDO:0005501)
Parent Node: developmental anomaly of metabolic origin (MONDO:0015327)
Parent Node: disorder of protein N-glycosylation (MONDO:0017740)
Parent Node: syndrome with a cerebellar malformation as major feature (MONDO:0017118)
Parent Node: syndromic neurometabolic disease with non-X-linked intellectual disability (MONDO:0015919)
..Starting node ..SLC39A8-CDG ()
Child Nodes:
Sister Nodes:
..3-methylglutaconic aciduria with cataracts, neurologic involvement and neutropenia ()
..adenylosuccinate lyase deficiency ()
..AICA-ribosiduria ()
..combined oxidative phosphorylation defect type 27 () L: 00519;
..guanidinoacetate methyltransferase deficiency ()
..leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome () L: 00418;
..non-X-linked congenital disorder of glycosylation with intellectual disability as a major feature ()
..PGM3-CDG ()
..sialidosis type 2 ()
..SLC39A8-CDG ()
..Smith-Lemli-Opitz syndrome ()
..Zellweger-like syndrome without peroxisomal anomalies ()
MONDO is developed by the Monarch Initiative. Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM,ClinVar, CTD

Term ID:

14746

Name:

SLC39A8-CDG

Definition:

Alternative IDs:

616721

ParentIDs:

TreeNumbers:

Synonyms:

carbohydrate deficient glycoprotein syndrome type IIn; CDG IIn; CDG syndrome type IIn; CDG-IIn; CDG2N; congenital disorder of glycosylation type 2n; congenital disorder of glycosylation type IIn; congenital disorder of glycosylation, type IIn; congenital disorder of glycosylation, type IIn; CDG2N; S

Slim Mappings:

Reference:

MedGen:
MeSH:
OMIM: 616721;
MSeqDR :
Genes:

Phenotypes

1	HP:0000007	Autosomal recessive inheritance
2	HP:0003577	Congenital onset
3	HP:0000483	Astigmatism
4	HP:0001272	Cerebellar atrophy
5	HP:0002059	Cerebral atrophy	HP:0040283
6	HP:0001363	Craniosynostosis	HP:0040283
7	HP:0001290	Generalized hypotonia
8	HP:0001263	Global developmental delay NAMDC: Mental retardation
9	HP:0001263	Global developmental delay NAMDC: Delayed development (evidence of at least one of A through F)
10	HP:0000365	Hearing impairment	HP:0040283
11	HP:0002540	Inability to walk
12	HP:0002187	Intellectual disability, profound
13	HP:0001382	Joint hypermobility	HP:0040283
14	HP:0000639	Nystagmus
15	HP:0000938	Osteopenia	HP:0040283
16	HP:0002719	Recurrent infections	HP:0040283
17	HP:0001250	Seizures NAMDC: Seizures	HP:0040283
18	HP:0004322	Short stature NAMDC: Short stature (patient��s height is below the 3rd percentile)
19	HP:0000486	Strabismus

Disease Causing ClinVar Variants

Variation_Name	GeneID	GeneSymbol	ClinicalSignificance	dbSNP	RCVaccession	TestedInGTR	PhenotypeIDs	Chromosome	Start	Stop	HGVS_g	OtherIDs	Disease_ClinVar
NM_001135146.2(SLC39A8):c.112G>C (p.Gly38Arg)	64116	SLC39A8	Pathogenic/Likely pathogenic	778210210	RCV000203234\|RCV001386978;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699\|MedGen:C3661900	4	103265708	103265708	NC_000004.11:g.103265708C>G	ClinVar:424755,ClinGen:CA249424,UniProtKB:Q9C0K1#VAR_076242,OMIM:608732.0001	C4225234 616721 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn;
NM_001135146.2(SLC39A8):c.1283C>T (p.Thr428Ile)	64116	SLC39A8	Pathogenic	142863074	RCV002246724;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103184301	103184301	103184301	-
NM_001135146.2(SLC39A8):c.218dup (p.Cys74fs)	64116	SLC39A8	Pathogenic	2149060093	RCV001580614;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103265601	103265602	103265601	-
NM_001135146.2(SLC39A8):c.1026T>A (p.Cys342Ter)	64116	SLC39A8	Likely pathogenic	1732173818	RCV001332454;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103189051	103189051	103189051	-
NM_001135146.2(SLC39A8):c.1019T>A (p.Ile340Asn)	64116	SLC39A8	Likely pathogenic	864309659	RCV000203240\|RCV000492852;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699\|MedGen:C3661900	4	103189058	103189058	4:g.103189058A>T	ClinVar:424755,ClinGen:CA277910,UniProtKB:Q9C0K1#VAR_076245,OMIM:608732.0002	C4225234 616721 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn;
NM_001135146.2(SLC39A8):c.338G>C (p.Cys113Ser)	64116	SLC39A8	Likely pathogenic	1444255127	RCV001089507;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103236869	103236869	4:g.103236869C>G	-
NM_001135146.2(SLC39A8):c.316C>T (p.Gln106Ter)	64116	SLC39A8	Likely pathogenic	1734625225	RCV001332455;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103236891	103236891	103236891	-
NM_001135146.2(SLC39A8):c.*1062C>T	64116	SLC39A8	Uncertain significance	-1	RCV003136780;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103183139	103183139	NC_000004.11:g.103183139G>A	-
NM_001135146.2(SLC39A8):c.1372G>C (p.Glu458Gln)	64116	SLC39A8	Uncertain significance	-1	RCV003136779;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103184212	103184212	NC_000004.11:g.103184212C>G	-
NM_001135146.2(SLC39A8):c.1166A>G (p.Asn389Ser)	64116	SLC39A8	Uncertain significance	146759817	RCV000487100\|RCV002226711\|RCV002526991;	N	MedGen:CN517202\|MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699\|MeSH:D030342,MedGen:C0950123	4	103188714	103188714	4:g.103188714T>C	ClinGen:CA3025499	CN169374 not specified;
NM_001135146.2(SLC39A8):c.1097dup (p.Leu366fs)	64116	SLC39A8	Uncertain significance	1553911693	RCV000497410\|RCV003139700;	N	MedGen:CN517202\|MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103188782	103188783	4:g.103188782_103188783insA	ClinGen:CA645372756	CN169374 not specified;
NM_001135146.2(SLC39A8):c.1020C>G (p.Ile340Met)	64116	SLC39A8	Uncertain significance	1732174032	RCV001332453;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103189057	103189057	103189057	-
NM_001135146.2(SLC39A8):c.965T>C (p.Ile322Thr)	64116	SLC39A8	Conflicting interpretations of pathogenicity	755786784	RCV001312045\|RCV002246293;	N	MedGen:C3661900\|MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103189112	103189112	103189112	-
NM_001135146.2(SLC39A8):c.923C>T (p.Thr308Met)	64116	SLC39A8	Uncertain significance	376000562	RCV001332456;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103189154	103189154	103189154	-
NM_001135146.2(SLC39A8):c.915G>C (p.Trp305Cys)	64116	SLC39A8	Uncertain significance	1578557666	RCV000984964;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103189162	103189162	4:g.103189162C>G	-
NM_001135146.2(SLC39A8):c.610G>T (p.Gly204Cys)	64116	SLC39A8	Conflicting interpretations of pathogenicity	779241085	RCV000203248\|RCV000733882\|RCV003226248;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699\|MedGen:C3661900\|MedGen:CN169374	4	103226211	103226211	4:g.103226211C>A	ClinVar:424757,ClinGen:CA249426,UniProtKB:Q9C0K1#VAR_076243,OMIM:608732.0004	C4225234 616721 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn;
NM_001135146.2(SLC39A8):c.552+48C>T	64116	SLC39A8	Benign	1462947	RCV001683810\|RCV001810228;	N	MedGen:C3661900\|MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103228545	103228545	103228545	-
NM_001135146.2(SLC39A8):c.500G>C (p.Gly167Ala)	64116	SLC39A8	Uncertain significance	1262995015	RCV002226857;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103228645	103228645	103228645	-
NM_001135146.2(SLC39A8):c.337T>C (p.Cys113Arg)	64116	SLC39A8	Uncertain significance	950101299	RCV000785949;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103236870	103236870	4:g.103236870A>G	-
NM_001135146.2(SLC39A8):c.16_28del (p.Ala6fs)	64116	SLC39A8	Uncertain significance	-1	RCV002471570;	N	MONDO:MONDO:0014746,MedGen:C4225234,OMIM:616721, Orphanet:468699	4	103265792	103265804	NC_000004.11:g.103265794_103265806del	-

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