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NC_000011.9:g.(?_45827353)_(47804770_?)del AND Leukocyte adhesion deficiency type II

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 15, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003119908.4

Allele description

NC_000011.9:g.(?_45827353)_(47804770_?)del

Genes:
  • ARFGAP2:ADP ribosylation factor GTPase activating protein 2 [Gene - OMIM - HGNC]
  • AGBL2:AGBL carboxypeptidase 2 [Gene - OMIM - HGNC]
  • C1QTNF4:C1q and TNF related 4 [Gene - OMIM - HGNC]
  • CELF1:CUGBP Elav-like family member 1 [Gene - OMIM - HGNC]
  • FREY1:Frey regulator of sperm-oocyte fusion 1 [Gene - HGNC]
  • LARGE2:LARGE xylosyl- and glucuronyltransferase 2 [Gene - OMIM - HGNC]
  • LRP4:LDL receptor related protein 4 [Gene - OMIM - HGNC]
  • MADD-AS1:MADD antisense RNA 1 [Gene - HGNC]
  • MADD:MAP kinase activating death domain [Gene - OMIM - HGNC]
  • NDUFS3:NADH:ubiquinone oxidoreductase core subunit S3 [Gene - OMIM - HGNC]
  • PHF21A:PHD finger protein 21A [Gene - OMIM - HGNC]
  • ARHGAP1:Rho GTPase activating protein 1 [Gene - OMIM - HGNC]
  • SPI1:Spi-1 proto-oncogene [Gene - OMIM - HGNC]
  • ACP2:acid phosphatase 2, lysosomal [Gene - OMIM - HGNC]
  • AMBRA1:autophagy and beclin 1 regulator 1 [Gene - OMIM - HGNC]
  • ATG13:autophagy related 13 [Gene - OMIM - HGNC]
  • CREB3L1:cAMP responsive element binding protein 3 like 1 [Gene - OMIM - HGNC]
  • CSTPP1:centriolar satellite-associated tubulin polyglutamylase complex regulator 1 [Gene - OMIM - HGNC]
  • CHRM4:cholinergic receptor muscarinic 4 [Gene - OMIM - HGNC]
  • F2:coagulation factor II, thrombin [Gene - OMIM - HGNC]
  • CRY2:cryptochrome circadian regulator 2 [Gene - OMIM - HGNC]
  • CKAP5:cytoskeleton associated protein 5 [Gene - OMIM - HGNC]
  • DDB2:damage specific DNA binding protein 2 [Gene - OMIM - HGNC]
  • DGKZ:diacylglycerol kinase zeta [Gene - OMIM - HGNC]
  • FAM180B:family with sequence similarity 180 member B [Gene - HGNC]
  • FNBP4:formin binding protein 4 [Gene - OMIM - HGNC]
  • HARBI1:harbinger transposase derived 1 [Gene - OMIM - HGNC]
  • KBTBD4:kelch repeat and BTB domain containing 4 [Gene - OMIM - HGNC]
  • MDK:midkine [Gene - OMIM - HGNC]
  • MTCH2:mitochondrial carrier 2 [Gene - OMIM - HGNC]
  • MAPK8IP1:mitogen-activated protein kinase 8 interacting protein 1 [Gene - OMIM - HGNC]
  • MYBPC3:myosin binding protein C3 [Gene - OMIM - HGNC]
  • NR1H3:nuclear receptor subfamily 1 group H member 3 [Gene - OMIM - HGNC]
  • NUP160:nucleoporin 160 [Gene - OMIM - HGNC]
  • PEX16:peroxisomal biogenesis factor 16 [Gene - OMIM - HGNC]
  • PSMC3:proteasome 26S subunit, ATPase 3 [Gene - OMIM - HGNC]
  • PACSIN3:protein kinase C and casein kinase substrate in neurons 3 [Gene - OMIM - HGNC]
  • PTPMT1:protein tyrosine phosphatase mitochondrial 1 [Gene - OMIM - HGNC]
  • RAPSN:receptor associated protein of the synapse [Gene - OMIM - HGNC]
  • SLC35C1:solute carrier family 35 member C1 [Gene - OMIM - HGNC]
  • SLC39A13:solute carrier family 39 member 13 [Gene - OMIM - HGNC]
  • ZNF408:zinc finger protein 408 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11p11.2
Genomic location:
Chr11: 45827353 - 47804770 (on Assembly GRCh37)
Preferred name:
NC_000011.9:g.(?_45827353)_(47804770_?)del
HGVS:
NC_000011.9:g.(?_45827353)_(47804770_?)del

Condition(s)

Name:
Leukocyte adhesion deficiency type II
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc; CDG IIc; Congenital disorder of glycosylation type 2C; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009953; MedGen: C0398739; Orphanet: 2968; Orphanet: 99843; OMIM: 266265

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795172Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 15, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Leukocyte adhesion deficiency II patients with a dual defect of the GDP-fucose transporter.

Helmus Y, Denecke J, Yakubenia S, Robinson P, Lühn K, Watson DL, McGrogan PJ, Vestweber D, Marquardt T, Wild MK.

Blood. 2006 May 15;107(10):3959-66. Epub 2006 Feb 2.

PubMed [citation]
PMID:
16455955

Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect.

Dauber A, Ercan A, Lee J, James P, Jacobs PP, Ashline DJ, Wang SR, Miller T, Hirschhorn JN, Nigrovic PA, Sackstein R.

Hum Mol Genet. 2014 Jun 1;23(11):2880-7. doi: 10.1093/hmg/ddu001. Epub 2014 Jan 8.

PubMed [citation]
PMID:
24403049
PMCID:
PMC4014190
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003795172.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SLC35C1-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the SLC35C1 gene has been identified. Loss-of-function variants in SLC35C1 are known to be pathogenic (PMID: 16455955, 24403049). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024