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NC_000011.9:g.(?_58916346)_(64972349_?)dup AND Leukocyte adhesion deficiency 3

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 21, 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:
RCV003113394.3

Allele description

NC_000011.9:g.(?_58916346)_(64972349_?)dup

Genes:
  • ARL2:ADP ribosylation factor like GTPase 2 [Gene - OMIM - HGNC]
  • AHNAK:AHNAK nucleoprotein [Gene - OMIM - HGNC]
  • BAD:BCL2 associated agonist of cell death [Gene - OMIM - HGNC]
  • BSCL2:BSCL2 lipid droplet biogenesis associated, seipin [Gene - OMIM - HGNC]
  • CD5:CD5 molecule [Gene - OMIM - HGNC]
  • CD6:CD6 molecule [Gene - OMIM - HGNC]
  • CDC42BPG:CDC42 binding protein kinase gamma [Gene - OMIM - HGNC]
  • DNAJC4:DnaJ heat shock protein family (Hsp40) member C4 [Gene - OMIM - HGNC]
  • EHD1:EH domain containing 1 [Gene - OMIM - HGNC]
  • EML3:EMAP like 3 [Gene - OMIM - HGNC]
  • FAM111A:FAM111 trypsin like peptidase A [Gene - OMIM - HGNC]
  • FAU:FAU ubiquitin like and ribosomal protein S30 fusion [Gene - OMIM - HGNC]
  • FERMT3:FERM domain containing kindlin 3 [Gene - OMIM - HGNC]
  • FKBP2:FKBP prolyl isomerase 2 [Gene - OMIM - HGNC]
  • GNG3:G protein subunit gamma 3 [Gene - OMIM - HGNC]
  • GPR137:G protein-coupled receptor 137 [Gene - HGNC]
  • LBHD1:LBH domain containing 1 [Gene - HGNC]
  • LRRN4CL:LRRN4 C-terminal like [Gene - HGNC]
  • NAALADL1:N-acetylated alpha-linked acidic dipeptidase like 1 [Gene - OMIM - HGNC]
  • NAA40:N-alpha-acetyltransferase 40, NatD catalytic subunit [Gene - OMIM - HGNC]
  • OTUB1:OTU deubiquitinase, ubiquitin aldehyde binding 1 [Gene - OMIM - HGNC]
  • PATL1:PAT1 homolog 1, processing body mRNA decay factor [Gene - OMIM - HGNC]
  • RAB3IL1:RAB3A interacting protein like 1 [Gene - HGNC]
  • RASGRP2:RAS guanyl releasing protein 2 [Gene - OMIM - HGNC]
  • RCOR2:REST corepressor 2 [Gene - OMIM - HGNC]
  • POLR2G:RNA polymerase II subunit G [Gene - OMIM - HGNC]
  • SAC3D1:SAC3 domain containing 1 [Gene - OMIM - HGNC]
  • TAF6L:TATA-box binding protein associated factor 6 like [Gene - OMIM - HGNC]
  • UBXN1:UBX domain protein 1 [Gene - OMIM - HGNC]
  • VPS37C:VPS37C subunit of ESCRT-I [Gene - OMIM - HGNC]
  • VPS51:VPS51 subunit of GARP complex [Gene - OMIM - HGNC]
  • WDR74:WD repeat domain 74 [Gene - OMIM - HGNC]
  • ASRGL1:asparaginase and isoaspartyl peptidase 1 [Gene - OMIM - HGNC]
  • ATL3:atlastin GTPase 3 [Gene - OMIM - HGNC]
  • ATG2A:autophagy related 2A [Gene - OMIM - HGNC]
  • BATF2:basic leucine zipper ATF-like transcription factor 2 [Gene - OMIM - HGNC]
  • BEST1:bestrophin 1 [Gene - OMIM - HGNC]
  • B3GAT3:beta-1,3-glucuronyltransferase 3 [Gene - OMIM - HGNC]
  • CAPN1:calpain 1 [Gene - OMIM - HGNC]
  • CATSPERZ:catsper channel auxiliary subunit zeta [Gene - OMIM - HGNC]
  • CDCA5:cell division cycle associated 5 [Gene - OMIM - HGNC]
  • CHRM1:cholinergic receptor muscarinic 1 [Gene - OMIM - HGNC]
  • CSKMT:citrate synthase lysine methyltransferase [Gene - OMIM - HGNC]
  • CPSF7:cleavage and polyadenylation specific factor 7 [Gene - HGNC]
  • CBLIF:cobalamin binding intrinsic factor [Gene - OMIM - HGNC]
  • CCDC86:coiled-coil domain containing 86 [Gene - OMIM - HGNC]
  • CCDC88B:coiled-coil domain containing 88B [Gene - OMIM - HGNC]
  • CYB561A3:cytochrome b561 family member A3 [Gene - OMIM - HGNC]
  • COX8A:cytochrome c oxidase subunit 8A [Gene - OMIM - HGNC]
  • DDB1:damage specific DNA binding protein 1 [Gene - OMIM - HGNC]
  • DTX4:deltex E3 ubiquitin ligase 4 [Gene - OMIM - HGNC]
  • DAGLA:diacylglycerol lipase alpha [Gene - OMIM - HGNC]
  • ESRRA:estrogen related receptor alpha [Gene - OMIM - HGNC]
  • EEF1G:eukaryotic translation elongation factor 1 gamma [Gene - OMIM - HGNC]
  • FADS1:fatty acid desaturase 1 [Gene - OMIM - HGNC]
  • FADS2:fatty acid desaturase 2 [Gene - OMIM - HGNC]
  • FADS3:fatty acid desaturase 3 [Gene - OMIM - HGNC]
  • FTH1:ferritin heavy chain 1 [Gene - OMIM - HGNC]
  • FLRT1:fibronectin leucine rich transmembrane protein 1 [Gene - OMIM - HGNC]
  • FEN1:flap structure-specific endonuclease 1 [Gene - OMIM - HGNC]
  • LGALS12:galectin 12 [Gene - OMIM - HGNC]
  • GANAB:glucosidase II alpha subunit [Gene - OMIM - HGNC]
  • PYGM:glycogen phosphorylase, muscle associated [Gene - OMIM - HGNC]
  • GPHA2:glycoprotein hormone subunit alpha 2 [Gene - OMIM - HGNC]
  • HNRNPUL2:heterogeneous nuclear ribonucleoprotein U like 2 [Gene - HGNC]
  • INCENP:inner centromere protein [Gene - OMIM - HGNC]
  • INTS5:integrator complex subunit 5 [Gene - OMIM - HGNC]
  • LRRC10B:leucine rich repeat containing 10B [Gene - HGNC]
  • MPEG1:macrophage expressed 1 [Gene - OMIM - HGNC]
  • MAJIN:membrane anchored junction protein [Gene - OMIM - HGNC]
  • MS4A10:membrane spanning 4-domains A10 [Gene - OMIM - HGNC]
  • MS4A12:membrane spanning 4-domains A12 [Gene - OMIM - HGNC]
  • MS4A13:membrane spanning 4-domains A13 [Gene - HGNC]
  • MS4A14:membrane spanning 4-domains A14 [Gene - HGNC]
  • MS4A15:membrane spanning 4-domains A15 [Gene - HGNC]
  • MS4A18:membrane spanning 4-domains A18 [Gene - HGNC]
  • MS4A1:membrane spanning 4-domains A1 [Gene - OMIM - HGNC]
  • MS4A2:membrane spanning 4-domains A2 [Gene - OMIM - HGNC]
  • MS4A3:membrane spanning 4-domains A3 [Gene - OMIM - HGNC]
  • MS4A4A:membrane spanning 4-domains A4A [Gene - OMIM - HGNC]
  • MS4A4E:membrane spanning 4-domains A4E [Gene - OMIM - HGNC]
  • MS4A5:membrane spanning 4-domains A5 [Gene - OMIM - HGNC]
  • MS4A6A:membrane spanning 4-domains A6A [Gene - OMIM - HGNC]
  • MS4A6E:membrane spanning 4-domains A6E [Gene - OMIM - HGNC]
  • MS4A7:membrane spanning 4-domains A7 [Gene - OMIM - HGNC]
  • MS4A8:membrane spanning 4-domains A8 [Gene - OMIM - HGNC]
  • MEN1:menin 1 [Gene - OMIM - HGNC]
  • MTA2:metastasis associated 1 family member 2 [Gene - OMIM - HGNC]
  • MIR192:microRNA 192 [Gene - OMIM - HGNC]
  • MIR194-2:microRNA 194-2 [Gene - OMIM - HGNC]
  • MARK2:microtubule affinity regulating kinase 2 [Gene - OMIM - HGNC]
  • MRPL16:mitochondrial ribosomal protein L16 [Gene - OMIM - HGNC]
  • MRPL49:mitochondrial ribosomal protein L49 [Gene - OMIM - HGNC]
  • MAP4K2:mitogen-activated protein kinase kinase kinase kinase 2 [Gene - OMIM - HGNC]
  • MACROD1:mono-ADP ribosylhydrolase 1 [Gene - OMIM - HGNC]
  • MYRF:myelin regulatory factor [Gene - OMIM - HGNC]
  • NRXN2:neurexin 2 [Gene - OMIM - HGNC]
  • NXF1:nuclear RNA export factor 1 [Gene - OMIM - HGNC]
  • NUDT22:nudix hydrolase 22 [Gene - HGNC]
  • OR10V1:olfactory receptor family 10 subfamily V member 1 [Gene - HGNC]
  • OR4D10:olfactory receptor family 4 subfamily D member 10 [Gene - HGNC]
  • OR4D11:olfactory receptor family 4 subfamily D member 11 [Gene - HGNC]
  • OR4D6:olfactory receptor family 4 subfamily D member 6 [Gene - HGNC]
  • OR4D9:olfactory receptor family 4 subfamily D member 9 [Gene - HGNC]
  • OR5A1:olfactory receptor family 5 subfamily A member 1 [Gene - HGNC]
  • OR5A2:olfactory receptor family 5 subfamily A member 2 [Gene - HGNC]
  • OR5AN1:olfactory receptor family 5 subfamily AN member 1 [Gene - OMIM - HGNC]
  • OOSP2:oocyte secreted protein 2 [Gene - OMIM - HGNC]
  • OSBP:oxysterol binding protein [Gene - OMIM - HGNC]
  • PGA3:pepsinogen A3 [Gene - OMIM - HGNC]
  • PGA4:pepsinogen A4 [Gene - OMIM - HGNC]
  • PGA5:pepsinogen A5 [Gene - OMIM - HGNC]
  • PRDX5:peroxiredoxin 5 [Gene - OMIM - HGNC]
  • PLAAT2:phospholipase A and acyltransferase 2 [Gene - OMIM - HGNC]
  • PLAAT3:phospholipase A and acyltransferase 3 [Gene - OMIM - HGNC]
  • PLAAT4:phospholipase A and acyltransferase 4 [Gene - OMIM - HGNC]
  • PLAAT5:phospholipase A and acyltransferase 5 [Gene - OMIM - HGNC]
  • PLCB3:phospholipase C beta 3 [Gene - OMIM - HGNC]
  • KCNK4:potassium two pore domain channel subfamily K member 4 [Gene - OMIM - HGNC]
  • PRPF19:pre-mRNA processing factor 19 [Gene - OMIM - HGNC]
  • PTGDR2:prostaglandin D2 receptor 2 [Gene - OMIM - HGNC]
  • PPP1R14B:protein phosphatase 1 regulatory inhibitor subunit 14B [Gene - OMIM - HGNC]
  • PPP2R5B:protein phosphatase 2 regulatory subunit B'beta [Gene - OMIM - HGNC]
  • RTN3:reticulon 3 [Gene - OMIM - HGNC]
  • ROM1:retinal outer segment membrane protein 1 [Gene - OMIM - HGNC]
  • RPS6KA4:ribosomal protein S6 kinase A4 [Gene - OMIM - HGNC]
  • SCGB1A1:secretoglobin family 1A member 1 [Gene - OMIM - HGNC]
  • SCGB1D1:secretoglobin family 1D member 1 [Gene - OMIM - HGNC]
  • SCGB1D2:secretoglobin family 1D member 2 [Gene - OMIM - HGNC]
  • SCGB1D4:secretoglobin family 1D member 4 [Gene - OMIM - HGNC]
  • SCGB2A1:secretoglobin family 2A member 1 [Gene - OMIM - HGNC]
  • SCGB2A2:secretoglobin family 2A member 2 [Gene - OMIM - HGNC]
  • SNHG1:small nucleolar RNA host gene 1 [Gene - OMIM - HGNC]
  • SNORD22:small nucleolar RNA, C/D box 22 [Gene - OMIM - HGNC]
  • SNORD25:small nucleolar RNA, C/D box 25 [Gene - OMIM - HGNC]
  • SNORD26:small nucleolar RNA, C/D box 26 [Gene - OMIM - HGNC]
  • SNORD27:small nucleolar RNA, C/D box 27 [Gene - OMIM - HGNC]
  • SNORD28:small nucleolar RNA, C/D box 28 [Gene - OMIM - HGNC]
  • SNORD29:small nucleolar RNA, C/D box 29 [Gene - OMIM - HGNC]
  • SNORD30:small nucleolar RNA, C/D box 30 [Gene - OMIM - HGNC]
  • SNORD31:small nucleolar RNA, C/D box 31 [Gene - OMIM - HGNC]
  • SLC15A3:solute carrier family 15 member 3 [Gene - OMIM - HGNC]
  • SLC22A10:solute carrier family 22 member 10 [Gene - OMIM - HGNC]
  • SLC22A11:solute carrier family 22 member 11 [Gene - OMIM - HGNC]
  • SLC22A12:solute carrier family 22 member 12 [Gene - OMIM - HGNC]
  • SLC22A24:solute carrier family 22 member 24 [Gene - OMIM - HGNC]
  • SLC22A25:solute carrier family 22 member 25 [Gene - OMIM - HGNC]
  • SLC22A6:solute carrier family 22 member 6 [Gene - OMIM - HGNC]
  • SLC22A8:solute carrier family 22 member 8 [Gene - OMIM - HGNC]
  • SLC22A9:solute carrier family 22 member 9 [Gene - OMIM - HGNC]
  • SLC3A2:solute carrier family 3 member 2 [Gene - OMIM - HGNC]
  • SNX15:sorting nexin 15 [Gene - OMIM - HGNC]
  • SPDYC:speedy/RINGO cell cycle regulator family member C [Gene - OMIM - HGNC]
  • SPINDOC:spindlin interactor and repressor of chromatin binding [Gene - HGNC]
  • SF1:splicing factor 1 [Gene - OMIM - HGNC]
  • SAXO4:stabilizer of axonemal microtubules 4 [Gene - OMIM - HGNC]
  • STIP1:stress induced phosphoprotein 1 [Gene - OMIM - HGNC]
  • SDHAF2:succinate dehydrogenase complex assembly factor 2 [Gene - OMIM - HGNC]
  • SYT7:synaptotagmin 7 [Gene - OMIM - HGNC]
  • SYVN1:synoviolin 1 [Gene - OMIM - HGNC]
  • STX3:syntaxin 3 [Gene - OMIM - HGNC]
  • STX5:syntaxin 5 [Gene - OMIM - HGNC]
  • TRMT112:tRNA methyltransferase activator subunit 11-2 [Gene - OMIM - HGNC]
  • TRPT1:tRNA phosphotransferase 1 [Gene - OMIM - HGNC]
  • TUT1:terminal uridylyl transferase 1, U6 snRNA-specific [Gene - OMIM - HGNC]
  • TTC9C:tetratricopeptide repeat domain 9C [Gene - HGNC]
  • TCN1:transcobalamin 1 [Gene - OMIM - HGNC]
  • TM7SF2:transmembrane 7 superfamily member 2 [Gene - OMIM - HGNC]
  • TMEM109:transmembrane protein 109 [Gene - OMIM - HGNC]
  • TMEM132A:transmembrane protein 132A [Gene - OMIM - HGNC]
  • TMEM138:transmembrane protein 138 [Gene - OMIM - HGNC]
  • TMEM179B:transmembrane protein 179B [Gene - HGNC]
  • TMEM216:transmembrane protein 216 [Gene - OMIM - HGNC]
  • TMEM223:transmembrane protein 223 [Gene - OMIM - HGNC]
  • TMEM258:transmembrane protein 258 [Gene - OMIM - HGNC]
  • TKFC:triokinase and FMN cyclase [Gene - OMIM - HGNC]
  • UQCC3:ubiquinol-cytochrome c reductase complex assembly factor 3 [Gene - OMIM - HGNC]
  • VEGFB:vascular endothelial growth factor B [Gene - OMIM - HGNC]
  • VWCE:von Willebrand factor C and EGF domains [Gene - OMIM - HGNC]
  • ZNHIT2:zinc finger HIT-type containing 2 [Gene - OMIM - HGNC]
  • ZBTB3:zinc finger and BTB domain containing 3 [Gene - HGNC]
  • ZFPL1:zinc finger protein like 1 [Gene - OMIM - HGNC]
  • ZFTA:zinc finger translocation associated [Gene - OMIM - HGNC]
  • ZP1:zona pellucida glycoprotein 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
11q12.1-13.1
Genomic location:
Chr11: 58916346 - 64972349 (on Assembly GRCh37)
Preferred name:
NC_000011.9:g.(?_58916346)_(64972349_?)dup
HGVS:
NC_000011.9:g.(?_58916346)_(64972349_?)dup

Condition(s)

Name:
Leukocyte adhesion deficiency 3
Synonyms:
INTEGRIN ACTIVATION DEFICIENCY DISEASE; LEUKOCYTE ADHESION DEFICIENCY 1 VARIANT; Leukocyte adhesion deficiency, type III
Identifiers:
MONDO: MONDO:0013016; MedGen: C2748536; Orphanet: 2968; Orphanet: 99844; OMIM: 612840

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795667Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 21, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003795667.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the FERMT3 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with FERMT3-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Dec 9, 2023