NC_000002.11:g.(?_72359356)_(74779761_?)del AND MOGS-congenital disorder of glycosylation

This record was updated by the submitter. Please see the current version.

Germline classification:: no classifications from unflagged records (1 submission)
Review status:: no classifications from unflagged records

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003109485.5

Allele description

NC_000002.11:g.(?_72359356)_(74779761_?)del

Genes:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
AUP1:AUP1 lipid droplet regulating VLDL assembly factor [Gene - OMIM - HGNC]
DQX1:DEAQ-box RNA dependent ATPase 1 [Gene - OMIM - HGNC]
FBXO41:F-box protein 41 [Gene - OMIM - HGNC]
HTRA2:HtrA serine peptidase 2 [Gene - OMIM - HGNC]
INO80B:INO80 complex subunit B [Gene - OMIM - HGNC]
MOB1A:MOB kinase activator 1A [Gene - OMIM - HGNC]
NAT8:N-acetyltransferase 8 (putative) [Gene - OMIM - HGNC]
NAT8B:N-acetyltransferase 8B (putative, gene/pseudogene) [Gene - OMIM - HGNC]
RAB11FIP5:RAB11 family interacting protein 5 [Gene - OMIM - HGNC]
SMYD5:SMYD family member 5 [Gene - OMIM - HGNC]
STAMBP:STAM binding protein [Gene - OMIM - HGNC]
TLX2:T cell leukemia homeobox 2 [Gene - OMIM - HGNC]
TPRKB:TP53RK binding protein [Gene - OMIM - HGNC]
WDR54:WD repeat domain 54 [Gene - HGNC]
WBP1:WW domain binding protein 1 [Gene - OMIM - HGNC]
ACTG2:actin gamma 2, smooth muscle [Gene - OMIM - HGNC]
BOLA3:bolA family member 3 [Gene - OMIM - HGNC]
CCT7:chaperonin containing TCP1 subunit 7 [Gene - OMIM - HGNC]
C2orf78:chromosome 2 open reading frame 78 [Gene - HGNC]
C2orf81:chromosome 2 open reading frame 81 [Gene - HGNC]
CCDC142:coiled-coil domain containing 142 [Gene - HGNC]
CYP26B1:cytochrome P450 family 26 subfamily B member 1 [Gene - OMIM - HGNC]
DGUOK:deoxyguanosine kinase [Gene - OMIM - HGNC]
DOK1:docking protein 1 [Gene - OMIM - HGNC]
DUSP11:dual specificity phosphatase 11 [Gene - OMIM - HGNC]
DCTN1:dynactin subunit 1 [Gene - OMIM - HGNC]
EGR4:early growth response 4 [Gene - OMIM - HGNC]
EMX1:empty spiracles homeobox 1 [Gene - OMIM - HGNC]
EXOC6B:exocyst complex component 6B [Gene - OMIM - HGNC]
LBX2:ladybird homeobox 2 [Gene - OMIM - HGNC]
LOXL3:lysyl oxidase like 3 [Gene - OMIM - HGNC]
MOGS:mannosyl-oligosaccharide glucosidase [Gene - OMIM - HGNC]
MTHFD2:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Gene - OMIM - HGNC]
MRPL53:mitochondrial ribosomal protein L53 [Gene - OMIM - HGNC]
NOTO:notochord homeobox [Gene - OMIM - HGNC]
PCGF1:polycomb group ring finger 1 [Gene - OMIM - HGNC]
PRADC1:protease associated domain containing 1 [Gene - OMIM - HGNC]
RTKN:rhotekin [Gene - OMIM - HGNC]
SPR:sepiapterin reductase [Gene - OMIM - HGNC]
SFXN5:sideroflexin 5 [Gene - OMIM - HGNC]
SLC4A5:solute carrier family 4 member 5 [Gene - OMIM - HGNC]
TET3:tet methylcytosine dioxygenase 3 [Gene - OMIM - HGNC]
TTC31:tetratricopeptide repeat domain 31 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p13.2-13.1

Genomic location:

Chr2: 72359356 - 74779761 (on Assembly GRCh37)

Preferred name:

NC_000002.11:g.(?_72359356)_(74779761_?)del

HGVS:

NC_000002.11:g.(?_72359356)_(74779761_?)del

Condition(s)

Name:: MOGS-congenital disorder of glycosylation
Synonyms:: CDG IIb; GLUCOSIDASE I DEFICIENCY; Congenital disorder of glycosylation type 2B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011629; MedGen: C1853736; Orphanet: 79330; OMIM: 606056

Recent activity

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Mus musculus ribosomal protein S6 kinase, polypeptide 2 (Rps6kb2), transcript va...
Mus musculus ribosomal protein S6 kinase, polypeptide 2 (Rps6kb2), transcript variant 3, non-coding RNA
gi|1340723194|ref|NR_153661.1|

Nucleotide
AAK83644 (0)
GEO DataSets
AAC50223 (0)
SRA
Zdhhc22 zinc finger, DHHC-type containing 22 [Mus musculus]
Zdhhc22 zinc finger, DHHC-type containing 22 [Mus musculus]
Gene ID:238331

Gene
238331[uid] AND (alive[prop]) (1)
Gene

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No clinical assertions found. See "Flagged submissions" below.

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glycosylation, hypogammaglobulinemia, and resistance to viral infections.

Sadat MA, Moir S, Chun TW, Lusso P, Kaplan G, Wolfe L, Memoli MJ, He M, Vega H, Kim LJY, Huang Y, Hussein N, Nievas E, Mitchell R, Garofalo M, Louie A, Ireland DC, Grunes C, Cimbro R, Patel V, Holzapfel G, Salahuddin D, et al.

N Engl J Med. 2014 Apr 24;370(17):1615-1625. doi: 10.1056/NEJMoa1302846. Epub 2014 Apr 9.

PubMed [citation]

PMID:: 24716661
PMCID:: PMC4066413

Mitotic Intragenic Recombination: A Mechanism of Survival for Several Congenital Disorders of Glycosylation.

Kane MS, Davids M, Adams C, Wolfe LA, Cheung HW, Gropman A, Huang Y; NISC Comparative Sequencing Program., Ng BG, Freeze HH, Adams DR, Gahl WA, Boerkoel CF.

Am J Hum Genet. 2016 Feb 4;98(2):339-46. doi: 10.1016/j.ajhg.2015.12.007. Epub 2016 Jan 21.

PubMed [citation]

PMID:: 26805780
PMCID:: PMC4746335

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003791461.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the MOGS gene has been identified. Loss-of-function variants in MOGS are known to be pathogenic (PMID: 24716661, 26805780). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with MOGS-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791461	Invitae	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791461 appears to be redundant with SCV003792832. (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 29, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24716661, 26805780, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791461

Invitae

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV003791461 appears to be redundant with SCV003792832.

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 29, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Last Updated: Feb 14, 2024

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