NC_000001.10:g.(?_149895434)_(156851434_?)dup AND Kostmann syndrome

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 2021
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:: RCV003120769.7

Allele description

NC_000001.10:g.(?_149895434)_(156851434_?)dup

Genes:

ADAM15:ADAM metallopeptidase domain 15 [Gene - OMIM - HGNC]
ADAMTSL4:ADAMTS like 4 [Gene - OMIM - HGNC]
ASH1L:ASH1 like histone lysine methyltransferase [Gene - OMIM - HGNC]
ATP8B2:ATPase phospholipid transporting 8B2 [Gene - OMIM - HGNC]
BNIPL:BCL2 interacting protein like [Gene - OMIM - HGNC]
C2CD4D:C2 calcium dependent domain containing 4D [Gene - HGNC]
CLK2:CDC like kinase 2 [Gene - OMIM - HGNC]
CKS1B:CDC28 protein kinase regulatory subunit 1B [Gene - OMIM - HGNC]
CDC42SE1:CDC42 small effector 1 [Gene - OMIM - HGNC]
CRTC2:CREB regulated transcription coactivator 2 [Gene - OMIM - HGNC]
CELF3:CUGBP Elav-like family member 3 [Gene - OMIM - HGNC]
DCST1:DC-STAMP domain containing 1 [Gene - OMIM - HGNC]
DCST2:DC-STAMP domain containing 2 [Gene - OMIM - HGNC]
DENND4B:DENN domain containing 4B [Gene - OMIM - HGNC]
GPATCH4:G-patch domain containing 4 (gene/pseudogene) [Gene - HGNC]
GABPB2:GA binding protein transcription factor subunit beta 2 [Gene - HGNC]
GATAD2B:GATA zinc finger domain containing 2B [Gene - OMIM - HGNC]
HAX1:HCLS1 associated protein X-1 [Gene - OMIM - HGNC]
HORMAD1:HORMA domain containing 1 [Gene - OMIM - HGNC]
IQGAP3:IQ motif containing GTPase activating protein 3 [Gene - HGNC]
KHDC4:KH domain containing 4, pre-mRNA splicing factor [Gene - OMIM - HGNC]
KPLCE:KPRP N-terminal and LCE C-terminal like protein [Gene - HGNC]
LYSMD1:LysM domain containing 1 [Gene - HGNC]
MCL1:MCL1 apoptosis regulator, BCL2 family member [Gene - OMIM - HGNC]
MINDY1:MINDY lysine 48 deubiquitinase 1 [Gene - OMIM - HGNC]
MIR9-1HG:MIR9-1 host gene [Gene - OMIM - HGNC]
MLLT11:MLLT11 transcription factor 7 cofactor [Gene - OMIM - HGNC]
NAXE:NAD(P)HX epimerase [Gene - OMIM - HGNC]
OTUD7B:OTU deubiquitinase 7B [Gene - OMIM - HGNC]
PBXIP1:PBX homeobox interacting protein 1 [Gene - OMIM - HGNC]
PMF1-BGLAP:PMF1-BGLAP readthrough [Gene - HGNC]
RAB13:RAB13, member RAS oncogene family [Gene - OMIM - HGNC]
RAB25:RAB25, member RAS oncogene family [Gene - OMIM - HGNC]
RORC:RAR related orphan receptor C [Gene - OMIM - HGNC]
RUSC1:RUN and SH3 domain containing 1 [Gene - OMIM - HGNC]
RUSC1-AS1:RUSC1 antisense RNA 1 [Gene - HGNC]
RIT1:Ras like without CAAX 1 [Gene - OMIM - HGNC]
RHBG:Rh family B glycoprotein [Gene - OMIM - HGNC]
ARHGEF2:Rho/Rac guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]
S100A10:S100 calcium binding protein A10 [Gene - OMIM - HGNC]
S100A11:S100 calcium binding protein A11 [Gene - OMIM - HGNC]
S100A12:S100 calcium binding protein A12 [Gene - OMIM - HGNC]
S100A13:S100 calcium binding protein A13 [Gene - OMIM - HGNC]
S100A14:S100 calcium binding protein A14 [Gene - OMIM - HGNC]
S100A16:S100 calcium binding protein A16 [Gene - OMIM - HGNC]
S100A1:S100 calcium binding protein A1 [Gene - OMIM - HGNC]
S100A2:S100 calcium binding protein A2 [Gene - OMIM - HGNC]
S100A3:S100 calcium binding protein A3 [Gene - OMIM - HGNC]
S100A4:S100 calcium binding protein A4 [Gene - OMIM - HGNC]
S100A5:S100 calcium binding protein A5 [Gene - OMIM - HGNC]
S100A6:S100 calcium binding protein A6 [Gene - OMIM - HGNC]
S100A7:S100 calcium binding protein A7 [Gene - OMIM - HGNC]
S100A7A:S100 calcium binding protein A7A [Gene - OMIM - HGNC]
S100A8:S100 calcium binding protein A8 [Gene - OMIM - HGNC]
S100A9:S100 calcium binding protein A9 [Gene - OMIM - HGNC]
SETDB1:SET domain bifurcated histone lysine methyltransferase 1 [Gene - OMIM - HGNC]
SH2D2A:SH2 domain containing 2A [Gene - OMIM - HGNC]
SHC1:SHC adaptor protein 1 [Gene - OMIM - HGNC]
SMG5:SMG5 nonsense mediated mRNA decay factor [Gene - OMIM - HGNC]
SNAPIN:SNAP associated protein [Gene - OMIM - HGNC]
SHE:Src homology 2 domain containing E [Gene - OMIM - HGNC]
TNFAIP8L2:TNF alpha induced protein 8 like 2 [Gene - OMIM - HGNC]
TSACC:TSSK6 activating cochaperone [Gene - OMIM - HGNC]
VHLL:VHL like [Gene - OMIM - HGNC]
YY1AP1:YY1 associated protein 1 [Gene - OMIM - HGNC]
ANP32E:acidic nuclear phosphoprotein 32 family member E [Gene - OMIM - HGNC]
ADAR:adenosine deaminase RNA specific [Gene - OMIM - HGNC]
ANXA9:annexin A9 [Gene - OMIM - HGNC]
APH1A:aph-1 homolog A, gamma-secretase subunit [Gene - OMIM - HGNC]
AQP10:aquaporin 10 [Gene - OMIM - HGNC]
ARNT:aryl hydrocarbon receptor nuclear translocator [Gene - OMIM - HGNC]
BGLAP:bone gamma-carboxyglutamate protein [Gene - OMIM - HGNC]
BCAN:brevican [Gene - OMIM - HGNC]
CREB3L4:cAMP responsive element binding protein 3 like 4 [Gene - OMIM - HGNC]
CA14:carbonic anhydrase 14 [Gene - OMIM - HGNC]
CTSK:cathepsin K [Gene - OMIM - HGNC]
CTSS:cathepsin S [Gene - OMIM - HGNC]
CRABP2:cellular retinoic acid binding protein 2 [Gene - OMIM - HGNC]
CERS2:ceramide synthase 2 [Gene - OMIM - HGNC]
CCT3:chaperonin containing TCP1 subunit 3 [Gene - OMIM - HGNC]
CHRNB2:cholinergic receptor nicotinic beta 2 subunit [Gene - OMIM - HGNC]
CHTOP:chromatin target of PRMT1 [Gene - OMIM - HGNC]
C1orf43:chromosome 1 open reading frame 43 [Gene - OMIM - HGNC]
C1orf54:chromosome 1 open reading frame 54 [Gene - HGNC]
C1orf56:chromosome 1 open reading frame 56 [Gene - HGNC]
CFAP141:cilia and flagella associated protein 141 [Gene - HGNC]
CGN:cingulin [Gene - OMIM - HGNC]
CIART:circadian associated repressor of transcription [Gene - OMIM - HGNC]
CRNN:cornulin [Gene - OMIM - HGNC]
CRCT1:cysteine rich C-terminal 1 [Gene - OMIM - HGNC]
DAP3:death associated protein 3 [Gene - OMIM - HGNC]
DPM3:dolichyl-phosphate mannosyltransferase subunit 3, regulatory [Gene - OMIM - HGNC]
ENTREP3:endosomal transmembrane epsin interactor 3 [Gene - OMIM - HGNC]
ENSA:endosulfine alpha [Gene - OMIM - HGNC]
EFNA1:ephrin A1 [Gene - OMIM - HGNC]
EFNA3:ephrin A3 [Gene - OMIM - HGNC]
EFNA4:ephrin A4 [Gene - OMIM - HGNC]
ECM1:extracellular matrix protein 1 [Gene - OMIM - HGNC]
FDPS:farnesyl diphosphate synthase [Gene - OMIM - HGNC]
FLG2:filaggrin 2 [Gene - OMIM - HGNC]
FLG:filaggrin [Gene - OMIM - HGNC]
FLAD1:flavin adenine dinucleotide synthetase 1 [Gene - OMIM - HGNC]
FALEC:focally amplified long non-coding RNA in epithelial cancer [Gene - OMIM - HGNC]
GBA1:glucosylceramidase beta 1 [Gene - OMIM - HGNC]
GLMP:glycosylated lysosomal membrane protein [Gene - OMIM - HGNC]
GOLPH3L:golgi phosphoprotein 3 like [Gene - OMIM - HGNC]
GON4L:gon-4 like [Gene - OMIM - HGNC]
HDGF:heparin binding growth factor [Gene - OMIM - HGNC]
HRNR:hornerin [Gene - OMIM - HGNC]
HAPLN2:hyaluronan and proteoglycan link protein 2 [Gene - OMIM - HGNC]
HCN3:hyperpolarization activated cyclic nucleotide gated potassium channel 3 [Gene - OMIM - HGNC]
INSRR:insulin receptor related receptor [Gene - OMIM - HGNC]
INTS3:integrator complex subunit 3 [Gene - OMIM - HGNC]
ISG20L2:interferon stimulated exonuclease gene 20 like 2 [Gene - OMIM - HGNC]
IL6R:interleukin 6 receptor [Gene - OMIM - HGNC]
ILF2:interleukin enhancer binding factor 2 [Gene - OMIM - HGNC]
IVL:involucrin [Gene - OMIM - HGNC]
JTB:jumping translocation breakpoint [Gene - OMIM - HGNC]
KRTCAP2:keratinocyte associated protein 2 [Gene - OMIM - HGNC]
KPRP:keratinocyte proline rich protein [Gene - OMIM - HGNC]
LMNA:lamin A/C [Gene - OMIM - HGNC]
LCE1A:late cornified envelope 1A [Gene - OMIM - HGNC]
LCE1B:late cornified envelope 1B [Gene - OMIM - HGNC]
LCE1C:late cornified envelope 1C [Gene - OMIM - HGNC]
LCE1D:late cornified envelope 1D [Gene - OMIM - HGNC]
LCE1E:late cornified envelope 1E [Gene - OMIM - HGNC]
LCE1F:late cornified envelope 1F [Gene - OMIM - HGNC]
LCE2A:late cornified envelope 2A [Gene - OMIM - HGNC]
LCE2B:late cornified envelope 2B [Gene - OMIM - HGNC]
LCE2C:late cornified envelope 2C [Gene - OMIM - HGNC]
LCE2D:late cornified envelope 2D [Gene - OMIM - HGNC]
LCE3A:late cornified envelope 3A [Gene - OMIM - HGNC]
LCE3B:late cornified envelope 3B [Gene - OMIM - HGNC]
LCE3C:late cornified envelope 3C [Gene - OMIM - HGNC]
LCE3D:late cornified envelope 3D [Gene - OMIM - HGNC]
LCE3E:late cornified envelope 3E [Gene - OMIM - HGNC]
LCE4A:late cornified envelope 4A [Gene - OMIM - HGNC]
LCE5A:late cornified envelope 5A [Gene - OMIM - HGNC]
LCE6A:late cornified envelope 6A [Gene - HGNC]
LELP1:late cornified envelope like proline rich 1 [Gene - OMIM - HGNC]
LAMTOR2:late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 [Gene - OMIM - HGNC]
LENEP:lens epithelial protein [Gene - OMIM - HGNC]
LINGO4:leucine rich repeat and Ig domain containing 4 [Gene - OMIM - HGNC]
LORICRIN:loricrin cornified envelope precursor protein [Gene - OMIM - HGNC]
MTX1:metaxin 1 [Gene - OMIM - HGNC]
METTL25B:methyltransferase like 25B [Gene - HGNC]
MEX3A:mex-3 RNA binding family member A [Gene - OMIM - HGNC]
MIR9-1:microRNA 9-1 [Gene - OMIM - HGNC]
MSTO1:misato mitochondrial distribution and morphology regulator 1 [Gene - OMIM - HGNC]
MRPL24:mitochondrial ribosomal protein L24 [Gene - OMIM - HGNC]
MRPL9:mitochondrial ribosomal protein L9 [Gene - OMIM - HGNC]
MRPS21:mitochondrial ribosomal protein S21 [Gene - OMIM - HGNC]
MUC1:mucin 1, cell surface associated [Gene - OMIM - HGNC]
MEF2D:myocyte enhancer factor 2D [Gene - OMIM - HGNC]
MTMR11:myotubularin related protein 11 [Gene - HGNC]
NPR1:natriuretic peptide receptor 1 [Gene - OMIM - HGNC]
NES:nestin [Gene - OMIM - HGNC]
NTRK1:neurotrophic receptor tyrosine kinase 1 [Gene - OMIM - HGNC]
NUP210L:nucleoporin 210 like [Gene - HGNC]
OAZ3:ornithine decarboxylase antizyme 3 [Gene - OMIM - HGNC]
PGLYRP3:peptidoglycan recognition protein 3 [Gene - OMIM - HGNC]
PGLYRP4:peptidoglycan recognition protein 4 [Gene - OMIM - HGNC]
PI4KB:phosphatidylinositol 4-kinase beta [Gene - OMIM - HGNC]
PIP5K1A:phosphatidylinositol-4-phosphate 5-kinase type 1 alpha [Gene - OMIM - HGNC]
PMVK:phosphomevalonate kinase [Gene - OMIM - HGNC]
PLEKHO1:pleckstrin homology domain containing O1 [Gene - OMIM - HGNC]
POGZ:pogo transposable element derived with ZNF domain [Gene - OMIM - HGNC]
PMF1:polyamine modulated factor 1 [Gene - OMIM - HGNC]
KCNN3:potassium calcium-activated channel subfamily N member 3 [Gene - OMIM - HGNC]
PRPF3:pre-mRNA processing factor 3 [Gene - OMIM - HGNC]
PAQR6:progestin and adipoQ receptor family member 6 [Gene - OMIM - HGNC]
PRR9:proline rich 9 [Gene - HGNC]
PRCC:proline rich mitotic checkpoint control factor [Gene - OMIM - HGNC]
PSMB4:proteasome 20S subunit beta 4 [Gene - OMIM - HGNC]
PSMD4:proteasome 26S subunit ubiquitin receptor, non-ATPase 4 [Gene - OMIM - HGNC]
PRUNE1:prune exopolyphosphatase 1 [Gene - OMIM - HGNC]
PYGO2:pygopus family PHD finger 2 [Gene - OMIM - HGNC]
PKLR:pyruvate kinase L/R [Gene - OMIM - HGNC]
RPRD2:regulation of nuclear pre-mRNA domain containing 2 [Gene - OMIM - HGNC]
RFX5:regulatory factor X5 [Gene - OMIM - HGNC]
RIIAD1:regulatory subunit of type II PKA R-subunit domain containing 1 [Gene - HGNC]
RXFP4:relaxin family peptide/INSL5 receptor 4 [Gene - OMIM - HGNC]
RPTN:repetin [Gene - OMIM - HGNC]
RPS27:ribosomal protein S27 [Gene - OMIM - HGNC]
SCAMP3:secretory carrier membrane protein 3 [Gene - OMIM - HGNC]
SELENBP1:selenium binding protein 1 [Gene - OMIM - HGNC]
SEMA4A:semaphorin 4A [Gene - OMIM - HGNC]
SEMA6C:semaphorin 6C [Gene - OMIM - HGNC]
SSR2:signal sequence receptor subunit 2 [Gene - OMIM - HGNC]
SPRR1A:small proline rich protein 1A [Gene - OMIM - HGNC]
SPRR1B:small proline rich protein 1B [Gene - OMIM - HGNC]
SPRR2A:small proline rich protein 2A [Gene - OMIM - HGNC]
SPRR2B:small proline rich protein 2B [Gene - OMIM - HGNC]
SPRR2D:small proline rich protein 2D [Gene - OMIM - HGNC]
SPRR2E:small proline rich protein 2E [Gene - OMIM - HGNC]
SPRR2F:small proline rich protein 2F [Gene - OMIM - HGNC]
SPRR2G:small proline rich protein 2G [Gene - OMIM - HGNC]
SPRR3:small proline rich protein 3 [Gene - OMIM - HGNC]
SPRR4:small proline rich protein 4 [Gene - OMIM - HGNC]
SCNM1:sodium channel modifier 1 [Gene - OMIM - HGNC]
SLC25A44:solute carrier family 25 member 44 [Gene - OMIM - HGNC]
SLC27A3:solute carrier family 27 member 3 [Gene - OMIM - HGNC]
SLC39A1:solute carrier family 39 member 1 [Gene - OMIM - HGNC]
SLC50A1:solute carrier family 50 member 1 [Gene - OMIM - HGNC]
SNX27:sorting nexin 27 [Gene - OMIM - HGNC]
SMCP:sperm mitochondria associated cysteine rich protein [Gene - OMIM - HGNC]
SF3B4:splicing factor 3b subunit 4 [Gene - OMIM - HGNC]
SYT11:synaptotagmin 11 [Gene - OMIM - HGNC]
TTC24:tetratricopeptide repeat domain 24 [Gene - HGNC]
THEM4:thioesterase superfamily member 4 [Gene - OMIM - HGNC]
THEM5:thioesterase superfamily member 5 [Gene - OMIM - HGNC]
TARS2:threonyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
THBS3:thrombospondin 3 [Gene - OMIM - HGNC]
TMEM79:transmembrane protein 79 [Gene - OMIM - HGNC]
TCHHL1:trichohyalin like 1 [Gene - HGNC]
TCHH:trichohyalin [Gene - OMIM - HGNC]
TRIM46:tripartite motif containing 46 [Gene - OMIM - HGNC]
TMOD4:tropomodulin 4 [Gene - OMIM - HGNC]
TPM3:tropomyosin 3 [Gene - OMIM - HGNC]
TDRKH:tudor and KH domain containing [Gene - OMIM - HGNC]
TDRD10:tudor domain containing 10 [Gene - HGNC]
TUFT1:tuftelin 1 [Gene - OMIM - HGNC]
UBQLN4:ubiquilin 4 [Gene - OMIM - HGNC]
UBAP2L:ubiquitin associated protein 2 like [Gene - OMIM - HGNC]
UBE2Q1:ubiquitin conjugating enzyme E2 Q1 [Gene - OMIM - HGNC]
LOC101928034:uncharacterized LOC101928034 [Gene]
VPS45:vacuolar protein sorting 45 homolog [Gene - OMIM - HGNC]
VPS72:vacuolar protein sorting 72 homolog [Gene - OMIM - HGNC]
ZBTB7B:zinc finger and BTB domain containing 7B [Gene - OMIM - HGNC]
ZNF687:zinc finger protein 687 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1q21.2-23.1

Genomic location:

Chr1: 149895434 - 156851434 (on Assembly GRCh37)

Preferred name:

NC_000001.10:g.(?_149895434)_(156851434_?)dup

HGVS:

NC_000001.10:g.(?_149895434)_(156851434_?)dup

Condition(s)

Name:: Kostmann syndrome (SCN3)
Synonyms:: Kostmann disease; Agranulocytosis infantile; Autosomal recessive severe congenital neutropenia type 3
Identifiers:: MONDO: MONDO:0012548; MedGen: C5235141; Orphanet: 99749; OMIM: 610738

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791413	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791413

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2021)

germline

clinical testing

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

Help

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

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, SCV003791413.1

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the HAX1 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 with HAX1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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

Last Updated: Sep 30, 2023

ClinVar

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