Aliases for NCLN Gene

Aliases for NCLN Gene

  • Nicalin 2 3 4 5
  • Nicastrin-Like Protein 2 3 4
  • Nicalin Homolog (Zebrafish) 2
  • Nicalin Homolog 3
  • NET59 3

External Ids for NCLN Gene

Previous GeneCards Identifiers for NCLN Gene

  • GC19P003139
  • GC19P002952

Summaries for NCLN Gene

GeneCards Summary for NCLN Gene

NCLN (Nicalin) is a Protein Coding gene. Diseases associated with NCLN include Hirschsprung Disease 1.

UniProtKB/Swiss-Prot Summary for NCLN Gene

  • May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning.

Gene Wiki entry for NCLN Gene

Additional gene information for NCLN Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NCLN Gene

Genomics for NCLN Gene

GeneHancer (GH) Regulatory Elements for NCLN Gene

Promoters and enhancers for NCLN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J003183 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 529.7 +2.0 1980 7.5 ZBTB40 ZNF217 SIN3A POLR2G USF1 PHF8 SIX5 PHB2 ZFX ZNF639 NCLN ZNF554 lnc-AES-8 CELF5
GH19J003175 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 526.5 -6.8 -6841 6.2 TCF12 SIN3A EP300 ZIC2 CLOCK POLR2A CTBP1 REST PRPF4 SREBF2 NCLN SF3A2 GNA15 APBA3 S1PR4 CACTIN-AS1 ENSG00000267139 GNA11 CACTIN ENSG00000268670
GH19J003198 Promoter 0.6 EPDnew 500.4 +13.3 13257 0.1 POLR2G AGO2 AGO1 NCLN CELF5 ZNF77
GH19J003210 Enhancer 1 Ensembl ENCODE 44.9 +25.3 25328 1 CTCF ZNF623 GABPA REST TRIM22 SMC3 HDAC2 ZNF341 POLR2A PCBP1 NCLN CACTIN ZNF77 SF3A2 S1PR4 GNA11 TLE6 CACTIN-AS1 CELF5
GH19J002968 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas 21.5 -213.8 -213806 6.7 USF1 ZNF10 ZNF263 AFF1 REST HES1 MYC TOE1 RUNX1 CTBP1 NCLN TLE6 TLE2 TLE5 ZNF77 GNA11 ENSG00000253392 ZNF57 S1PR4 ENSG00000267283
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NCLN on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NCLN

Top Transcription factor binding sites by QIAGEN in the NCLN gene promoter:
  • C/EBPalpha
  • HEN1
  • HOXA5
  • HSF1 (long)
  • HSF1short
  • NRSF form 1
  • NRSF form 2
  • Pax-5
  • PPAR-alpha

Genomic Locations for NCLN Gene

Genomic Locations for NCLN Gene
chr19:3,185,563-3,209,575
(GRCh38/hg38)
Size:
24,013 bases
Orientation:
Plus strand
chr19:3,185,561-3,209,573
(GRCh37/hg19)
Size:
24,013 bases
Orientation:
Plus strand

Genomic View for NCLN Gene

Genes around NCLN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NCLN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NCLN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NCLN Gene

Proteins for NCLN Gene

  • Protein details for NCLN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q969V3-NCLN_HUMAN
    Recommended name:
    Nicalin
    Protein Accession:
    Q969V3
    Secondary Accessions:
    • D6W613
    • O75252
    • Q6FI60
    • Q6ZMB7
    • Q8TAT7
    • Q96H48
    • Q96IS7
    • Q9BQH9
    • Q9BTX4
    • Q9NPP2

    Protein attributes for NCLN Gene

    Size:
    563 amino acids
    Molecular mass:
    62974 Da
    Quaternary structure:
    • Forms a complex with NOMO2 and TMEM147, resulting in a stabilization of the 3 proteins, which are otherwise quickly degraded by the proteasome. Due to the strong similarity between NOMO1, NOMO2 and NOMO3, probably also interacts with NOMO1 and NOMO3. Participates in a large protein complex, which is not related to the gamma-secretase complex.
    SequenceCaution:
    • Sequence=AAH03076.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH25926.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAB66502.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for NCLN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NCLN Gene

Post-translational modifications for NCLN Gene

  • Glycosylation at Asn241 and Asn428
  • Ubiquitination at Lys99, Lys471, and Lys491
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for NCLN Gene

Domains & Families for NCLN Gene

Gene Families for NCLN Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for NCLN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NCLN Gene

GenScript: Design optimal peptide antigens:
  • Nicastrin-like protein (NCLN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q969V3

UniProtKB/Swiss-Prot:

NCLN_HUMAN :
  • Belongs to the nicastrin family.
Family:
  • Belongs to the nicastrin family.
genes like me logo Genes that share domains with NCLN: view

Function for NCLN Gene

Molecular function for NCLN Gene

UniProtKB/Swiss-Prot Function:
May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning.

Phenotypes From GWAS Catalog for NCLN Gene

Gene Ontology (GO) - Molecular Function for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17261586
genes like me logo Genes that share ontologies with NCLN: view
genes like me logo Genes that share phenotypes with NCLN: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NCLN

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NCLN Gene

Localization for NCLN Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCLN Gene

Endoplasmic reticulum membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NCLN gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 2
nucleus 2
extracellular 1
cytoskeleton 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Lipid droplets (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IDA,IBA 20538592
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
GO:0032991 protein-containing complex IDA 20538592
genes like me logo Genes that share ontologies with NCLN: view

Pathways & Interactions for NCLN Gene

PathCards logo

SuperPathways for NCLN Gene

No Data Available

Gene Ontology (GO) - Biological Process for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009966 regulation of signal transduction IEA,IBA 21873635
GO:0043254 regulation of protein complex assembly IDA 20538592
GO:0050821 protein stabilization IMP 20538592
GO:0061635 regulation of protein complex stability IDA 20538592
genes like me logo Genes that share ontologies with NCLN: view

No data available for Pathways by source and SIGNOR curated interactions for NCLN Gene

Drugs & Compounds for NCLN Gene

No Compound Related Data Available

Transcripts for NCLN Gene

mRNA/cDNA for NCLN Gene

2 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NCLN

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NCLN Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b · 17c · 17d ^
SP1: - - - - -
SP2: - - -
SP3: - - -
SP4: - - - - - -
SP5: - -
SP6: - -
SP7:
SP8:

ExUns: 18
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for NCLN Gene

GeneLoc Exon Structure for
NCLN

Expression for NCLN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NCLN Gene

Protein differential expression in normal tissues from HIPED for NCLN Gene

This gene is overexpressed in Neutrophil (7.6) and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NCLN Gene



Protein tissue co-expression partners for NCLN Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NCLN

SOURCE GeneReport for Unigene cluster for NCLN Gene:

Hs.657032

mRNA Expression by UniProt/SwissProt for NCLN Gene:

Q969V3-NCLN_HUMAN
Tissue specificity: Highly expressed in pancreas and skeletal muscle and, at lower levels, in heart.

Evidence on tissue expression from TISSUES for NCLN Gene

  • Nervous system(4.6)
  • Kidney(4.2)
  • Intestine(3.1)
genes like me logo Genes that share expression patterns with NCLN: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCLN Gene

Orthologs for NCLN Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NCLN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCLN 31 30
  • 98.64 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NCLN 31 30
  • 90.29 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NCLN 31
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NCLN 31 30
  • 89.09 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ncln 30
  • 87.21 (n)
mouse
(Mus musculus)
Mammalia Ncln 17 31 30
  • 87.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NCLN 31
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves NCLN 31 30
  • 73.5 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NCLN 31
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ncln 30
  • 72.86 (n)
Str.1209 30
zebrafish
(Danio rerio)
Actinopterygii ncl1 31 30
  • 73.65 (n)
OneToOne
wufb07e09 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002549 30
  • 53.46 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4972 31 30
  • 48.2 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea nra-2 31 30
  • 41.38 (n)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G44330 30
  • 44.56 (n)
rice
(Oryza sativa)
Liliopsida Os08g0102100 30
  • 46.09 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10535 31
  • 36 (a)
OneToOne
Species where no ortholog for NCLN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NCLN Gene

ENSEMBL:
Gene Tree for NCLN (if available)
TreeFam:
Gene Tree for NCLN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NCLN: view image

Paralogs for NCLN Gene

No data available for Paralogs for NCLN Gene

Variants for NCLN Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NCLN Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs1057519322 Likely Pathogenic: Hirschsprung disease 1 3,193,404(+) C/T NONSENSE
rs11671067 - p.Glu214Asp
rs2288949 - p.Lys551Arg

Additional dbSNP identifiers (rs#s) for NCLN Gene

Structural Variations from Database of Genomic Variants (DGV) for NCLN Gene

Variant ID Type Subtype PubMed ID
nsv509716 CNV insertion 20534489
nsv953948 CNV deletion 24416366

Variation tolerance for NCLN Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.43; 81.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCLN Gene

Human Gene Mutation Database (HGMD)
NCLN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCLN

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NCLN Gene

Disorders for NCLN Gene

MalaCards: The human disease database

(1) MalaCards diseases for NCLN Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
- elite association - COSMIC cancer census association via MalaCards
Search NCLN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NCLN

genes like me logo Genes that share disorders with NCLN: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NCLN Gene

Publications for NCLN Gene

  1. The Nicastrin-like protein Nicalin regulates assembly and stability of the Nicalin-nodal modulator (NOMO) membrane protein complex. (PMID: 17261586) Haffner C … Haass C (The Journal of biological chemistry 2007) 2 3 23 54
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 54
  3. Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex. (PMID: 20538592) Dettmer U … Haffner C (The Journal of biological chemistry 2010) 3 4 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 54

Products for NCLN Gene

Sources for NCLN Gene