NCAM1

gene
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Also known as NCAMCD56

Summary

NCAM1 (neural cell adhesion molecule 1, HGNC:7656) is a protein-coding gene on chromosome 11q23.2, encoding Neural cell adhesion molecule 1 (P13591). This protein is a cell adhesion molecule involved in neuron-neuron adhesion, neurite fasciculation, outgrowth of neurites, etc.

This gene encodes a cell adhesion protein which is a member of the immunoglobulin superfamily. The encoded protein is involved in cell-to-cell interactions as well as cell-matrix interactions during development and differentiation. The encoded protein plays a role in the development of the nervous system by regulating neurogenesis, neurite outgrowth, and cell migration. This protein is also involved in the expansion of T lymphocytes, B lymphocytes and natural killer (NK) cells which play an important role in immune surveillance. This protein plays a role in signal transduction by interacting with fibroblast growth factor receptors, N-cadherin and other components of the extracellular matrix and by triggering signalling cascades involving FYN-focal adhesion kinase (FAK), mitogen-activated protein kinase (MAPK), and phosphatidylinositol 3-kinase (PI3K). One prominent isoform of this gene, cell surface molecule CD56, plays a role in several myeloproliferative disorders such as acute myeloid leukemia and differential expression of this gene is associated with differential disease progression. For example, increased expression of CD56 is correlated with lower survival in acute myeloid leukemia patients whereas increased severity of COVID-19 is correlated with decreased abundance of CD56-expressing NK cells in peripheral blood. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms.

Source: NCBI Gene 4684 — RefSeq curated summary.

At a glance

  • GWAS associations: 50
  • Clinical variants (ClinVar): 54 total — 1 pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_181351

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7656
Approved symbolNCAM1
Nameneural cell adhesion molecule 1
Location11q23.2
Locus typegene with protein product
StatusApproved
AliasesNCAM, CD56
Ensembl geneENSG00000149294
Ensembl biotypeprotein_coding
OMIM116930
Entrez4684

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 15 protein_coding, 6 retained_intron, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000316851, ENST00000401611, ENST00000524916, ENST00000525355, ENST00000525691, ENST00000525973, ENST00000526322, ENST00000528158, ENST00000528590, ENST00000529356, ENST00000530090, ENST00000530543, ENST00000531044, ENST00000531817, ENST00000533073, ENST00000533226, ENST00000534046, ENST00000534516, ENST00000611284, ENST00000613217, ENST00000615525, ENST00000617166, ENST00000619839, ENST00000620046, ENST00000621128, ENST00000621850

RefSeq mRNA: 30 — MANE Select: NM_181351 NM_000615, NM_001076682, NM_001242607, NM_001242608, NM_001386289, NM_001386290, NM_001386291, NM_001386292, NM_001400603, NM_001400604, NM_001400605, NM_001400606, NM_001400607, NM_001400608, NM_001400609, NM_001400610, NM_001400611, NM_001400612, NM_001400613, NM_001400615, NM_001400616, NM_001400617, NM_001400618, NM_001400619, NM_001400620, NM_001400621, NM_001400622, NM_001400623, NM_001400624, NM_181351

CCDS: CCDS73384, CCDS73385, CCDS73386, CCDS73387, CCDS73388, CCDS91595

Canonical transcript exons

ENST00000316851 — 20 exons

ExonStartEnd
ENSE00003471992113221296113221325
ENSE00003479684113206043113206180
ENSE00003492790113271760113271876
ENSE00003494379113202379113202453
ENSE00003502948113260146113260323
ENSE00003533558113232170113232354
ENSE00003584378113231645113231795
ENSE00003611511113207833113208002
ENSE00003643236113232718113232814
ENSE00003649418113270188113270395
ENSE00003653453113205523113205666
ENSE00003655908113207261113207378
ENSE00003681514113204286113204504
ENSE00003691564113235033113235164
ENSE00003693988113214369113214511
ENSE00003723845113275267113278436
ENSE00003724801113233147113233317
ENSE00003726501113246368113246370
ENSE00003747920113255877113256001
ENSE00003906045112961420112961664

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 99.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.3230 / max 2279.5144, expressed in 1034 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
11672739.18881005
1167282.6151476
1167262.5266513
2064490.8985306
1167450.7884103
1167420.4004182
1167410.3297179
1167440.307958
1167430.267792

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.64gold quality
ventricular zoneUBERON:000305399.00gold quality
ganglionic eminenceUBERON:000402398.97gold quality
middle temporal gyrusUBERON:000277198.95gold quality
entorhinal cortexUBERON:000272898.76gold quality
corpus callosumUBERON:000233698.67gold quality
endothelial cellCL:000011598.62gold quality
Brodmann (1909) area 46UBERON:000648398.56gold quality
ponsUBERON:000098898.52gold quality
superior frontal gyrusUBERON:000266198.50gold quality
prefrontal cortexUBERON:000045198.47gold quality
parietal lobeUBERON:000187298.41gold quality
C1 segment of cervical spinal cordUBERON:000646998.41gold quality
temporal lobeUBERON:000187198.37gold quality
postcentral gyrusUBERON:000258198.35gold quality
ventral tegmental areaUBERON:000269198.32gold quality
Brodmann (1909) area 9UBERON:001354098.24gold quality
spinal cordUBERON:000224098.22gold quality
frontal cortexUBERON:000187098.18gold quality
cerebral cortexUBERON:000095698.14gold quality
telencephalonUBERON:000189398.12gold quality
Ammon’s hornUBERON:000195498.12gold quality
neocortexUBERON:000195098.11gold quality
caudate nucleusUBERON:000187398.09gold quality
amygdalaUBERON:000187698.09gold quality
substantia nigra pars reticulataUBERON:000196698.09gold quality
superior vestibular nucleusUBERON:000722798.07gold quality
Brodmann (1909) area 23UBERON:001355498.03gold quality
nucleus accumbensUBERON:000188298.00gold quality
putamenUBERON:000187497.97gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-ANND-2yes1530.88
E-HCAD-56yes1387.46
E-MTAB-6678yes671.15
E-GEOD-84465yes27.23
E-CURD-112yes16.30
E-MTAB-8410yes16.01
E-MTAB-7316yes13.67
E-ANND-3yes6.52
E-MTAB-11268no1198.77
E-MTAB-7303no827.99
E-GEOD-93593no15.57

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ALX4, ARID1B, BARX1, BARX2, BTBD3, CEBPB, CUX1, CUX2, DMRTA1, HOXA1, HOXB9, HOXC6, HOXC8, HR, IRF9, JUN, LEF1, MYC, NFKB1, NFKB, NFKBIZ, NSD2, OTX2, PAX2, PAX5, PAX6, PAX8, PHOX2A, RELA, RUNX1, SOX2, SOX4, SP1, TP73

miRNA regulators (miRDB)

203 targeting NCAM1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3163100.0077.238605
HSA-MIR-8485100.0077.574731
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-6833-3P100.0070.633197
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3924100.0072.092394
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-511-3P99.9968.851467
HSA-MIR-186-5P99.9970.833707
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-480399.9871.993117
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-1213699.9872.815713
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548P99.9872.253784

Literature-anchored findings (GeneRIF, showing 40)

  • NCAM 105-115 kDa is a protease- and neuraminidase-susceptible fragment and was correlated with ventricular enlargement in chronic schizophrenia (p = 0.01). Release of NCAM fragments in schizophrenia may be part of the pathogenic mechanism. (PMID:11681838)
  • Significance of cell adhesion molecules, CD56/NCAM in particular, in human tumor growth and spreading. (PMID:11820619)
  • exists in lipid microdomains and transducts cell signalings via regulating the activation of signal transduction molecules (PMID:11915324)
  • PSA-NCAM was found to be expressed in the somata, dendrites and axonal processes of some neurons, which were identified as chandelier cell axon terminals (chandelier terminals), in the adult human entorhinal cortex and neocortex. (PMID:12003861)
  • CD56 expression predicts occurrence of CNS disease in acute lymphoblastic leukemia but not CR or survival. CD56 may enable targeting of leukemic cells to tissues that express it. (PMID:12008081)
  • CD56 molecules on NK cells interact with fibroblast growth factor receptor 1 on Jurkat T cells to trigger IL-2 production. (PMID:12121226)
  • Preferential apoptosis of CD56dim natural killer cell subset in patients with cancer. (PMID:12594840)
  • a useful immunohistochemical marker of Merkel cell carcinoma (PMID:12727026)
  • which the polysialyltransferases bind to the first fibronectin type III repeat (FN1) of NCAM to polymerize polysialic acid chains on appropriately presented glycans in adjacent regions. (PMID:12791681)
  • Strong overexpression of NCAM(CD56) and RUNX1(AML1) is a constant and characteristic feature of cardiomyocytes within or adjacent to scars in ICM. (PMID:12937148)
  • Natural killer (NK) cells expressing high CD56 levels are terminally differentiated cells identical to mature NK cells recently activated in the presence of IL-12, and not a functionally distinct subset or progenitors to mature CD56+low NK cells. (PMID:14688313)
  • there are two types of CD56+ epithelial cells in the pancreatic duct system: CD56+ endocrine cells are numerous during the early stage of gestation while CD56+ luminal cells may represent developmental and regenerative changes of pancreatic ducts. (PMID:14726964)
  • CD56 is expressed in bone marrow of acute myelogenous leukemias but not acute lymphoblastic leukemia (PMID:14959847)
  • Alzheimer patients presented values of low molecular weight-NCAM and high molecular weight-NCAM significantly higher than healthy controls of similar age (higher than 130 kDa) (PMID:15006709)
  • genetic variations in neural cell adhesion molecule 1 or nearby genes could confer risks associated with bipolar affective disorder in Japanese individuals. (PMID:15050861)
  • REVIEW: Prognostic significance of CD56 expressed in multiple myeloma (PMID:15061198)
  • CD56 expression was associated with the leukemogenetic mutation at the primitive hematopoietic progenitor cell level (PMID:15223636)
  • Unlike wild-type FGFR4, pituitary tumor derived-FGFR4 does not associate with neural cell-adhesion molecule (NCAM). (PMID:15231874)
  • Cells expressing this antigen repond to a Wilms tumor cell line feeder cells and are precursors of NK cells. (PMID:15246157)
  • Pre-activated, adherent-natural killer cells express low levels of CD56 and CD161 (PMID:15356097)
  • There is a close relationship between PSA-NCAM expression and neuronal migration. (PMID:15459479)
  • CD56bright natural killer cells accumulate in inflammatory lesions and, in the appropriate cytokine environment, can engage with CD14+ monocytes in a reciprocal activatory fashion, thereby amplifying the inflammatory response. (PMID:15528382)
  • first pediatric case describing coexpression of CD56 on B-lineage acute lymphoblastic leukemia (PMID:15626024)
  • CD56 seems to be the most sensitive marker for the diagnosis of SCC of the uterine cervix (PMID:15782066)
  • A significant increase was observed in PSA-NCAM, NCAM-180, NCAM-140, and HSP70 expression as seen by Western blotting and immunocytofluorescent studies in NMDA-treated cultures. (PMID:15950781)
  • polysialyltransferase ST8Sia IV/PST recognizes specific amino acids in the first fibronectin type III repeat of the neural cell adhesion molecule (PMID:16027151)
  • analysis of polymerization of polysialic acid on neural cell adhesion molecules (PMID:16172115)
  • NCAM is associated not only with a cell-to-cell adhesion mechanism, but also with tumorigenesis, including growth, development and perineural invasion in human salivary gland tumors (PMID:16211277)
  • CD56(bright) and CD56(dim) human natural killer-cell subsets exert different functional and cytotoxic activities in response to a live bacterial pathogen. (PMID:16316416)
  • The new role of Neural Cell Adhesion Molecules in tumor neo-angiogenesis relevant for endothelial cell organization into capillary-like structures. (PMID:16406048)
  • NCAM is hyposialylated in hereditary inclusion body myopathy skeletal) muscle. (PMID:16534119)
  • Tests whether activation and expansion of human NK cells with lipopolysaccharide (LPS) reveals differences between identical twins with regaard to C56 antigen. (PMID:16572491)
  • The gene expression profile of hepatic stem cells throughout life consists of high levels of expression of neuronal cell adhesion molecule (NCAM). (PMID:16627685)
  • identified co-induction of NKG2A and CD56 on activation of TH2 cells (PMID:16690409)
  • Isolation of 3 novel isoforms of AML 1 (RUNX1) with different transactivating function, that might be a regulatory element of the NCAM (CD56) overexpression in chronic myocardial ischemia. (PMID:16892559)
  • the FN1 alpha-helix is involved in an Ig5-FN1 interaction that is critical for the correct positioning of Ig5 N-glycans for polysialylation (PMID:17003032)
  • Co-immunoprecipitation and co-clustering paradigms were used to show that both NCAM and N-cadherin can interact with the 3Ig IIIC isoform of the FGFR1 in a number of cell types. (PMID:17005551)
  • NCAM1 along with RUNX1 is overexpressed during stress hematopoiesis in Down syndrome children and may contribute to the development of overt leukemia. (PMID:17043020)
  • In the “Europe only” stratum, there were nominally significant associations with five contiguous SNPs. (PMID:17161382)
  • Neuroblastoma cells resistant to anticancer drugs have increased invasive capacity caused by down-regulation of NCAM adhesion receptor. (PMID:17181871)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioncam1bENSDARG00000007220
danio_rerioncam1aENSDARG00000056181
mus_musculusNcam1ENSMUSG00000039542
rattus_norvegicusNcam1ENSRNOG00000031890

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9B (ENSG00000080854), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CNTN6 (ENSG00000134115), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), PRTG (ENSG00000166450), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), IGDCC3 (ENSG00000174498), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

Neural cell adhesion molecule 1P13591 (reviewed: P13591)

All UniProt accessions (12): P13591, A0A087WTR3, A0A087WVD0, A0A087WVU1, A0A087WWD4, A0A087WWJ5, A0A087WZS4, A0A087X1V2, A0A0C4DGS4, A0A0D9SF30, A0A0D9SF98, H7BYX6

UniProt curated annotations — full annotation on UniProt →

Function. This protein is a cell adhesion molecule involved in neuron-neuron adhesion, neurite fasciculation, outgrowth of neurites, etc. (Microbial infection) Acts as a receptor for rabies virus. (Microbial infection) Acts as a receptor for Zika virus.

Subunit / interactions. (Microbial infection) Interacts with rabies virus glycoprotein. (Microbial infection) Interacts with Zika virus envelope protein E. Interacts with MDK. Found in a complex with SLC39A6, SLC39A10 and with NCAM1; this complex controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-tomesenchymal transition. Interacts with synaptic plasticity regulator PANTS.

Subcellular location. Cell membrane Cell membrane Cell membrane Cell membrane Secreted Secreted.

Post-translational modifications. Polysialylated at Asn-459 and Asn-488 by ST8SIA2 and ST8SIA4. Polysialylation modulates cell interactions by confering both attractive and repulsive properties that are highly regulated by ST8SIA2 and ST8SIA4. Polysialylation is formed on a-2,3-linked sialic acid of core glycans.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (6)

UniProt IDNamesCanonical?
P13591-21yes
P13591-12, N-CAM 140
P13591-33, N-CAM 120
P13591-44
P13591-55, C
P13591-66

RefSeq proteins (30): NP_000606, NP_001070150, NP_001229536, NP_001229537, NP_001373218, NP_001373219, NP_001373220, NP_001373221, NP_001387532, NP_001387533, NP_001387534, NP_001387535, NP_001387536, NP_001387537, NP_001387538, NP_001387539, NP_001387540, NP_001387541, NP_001387542, NP_001387544, NP_001387545, NP_001387546, NP_001387547, NP_001387548, NP_001387549, NP_001387550, NP_001387551, NP_001387552, NP_001387553, NP_851996* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR003961FN3_domDomain
IPR007110Ig-like_domDomain
IPR009138Neural_cell_adhFamily
IPR013098Ig_I-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily

Pfam: PF00041, PF07679, PF13927

UniProt features (89 total): strand 33, splice variant 8, sequence conflict 8, domain 7, glycosylation site 6, disulfide bond 5, sequence variant 4, mutagenesis site 3, helix 3, compositionally biased region 2, modified residue 2, topological domain 2, lipid moiety-binding region 2, signal peptide 1, chain 1, region of interest 1, transmembrane region 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
2HAZX-RAY DIFFRACTION1.7
3MTRX-RAY DIFFRACTION1.8
5AEAX-RAY DIFFRACTION1.9
2E3VX-RAY DIFFRACTION1.95
2VKWX-RAY DIFFRACTION2.3
2VKXX-RAY DIFFRACTION2.7
5LKNSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P13591-F179.940.54

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 780, 784, 741, 706

Disulfide bonds (5): 41–96, 139–189, 235–287, 329–395, 436–489

Glycosylation sites (6): 222, 315, 347, 433, 459, 488

Mutagenesis-validated functional residues (3):

PositionPhenotype
433loss of polysialic acid addition by st8sia4; when associated with q-459 and q-488. loss of polysialic acid addition by s
459loss of polysialic acid addition by st8sia4; when associated with q-433 and q-488. loss of polysialic acid addition by s
488loss of polysialic acid addition by st8sia4; when associated with q-433 and q-459. loss of polysialic acid addition by s

Function

Pathways and Gene Ontology

Reactome pathways

17 pathways

IDPathway
R-HSA-3000178ECM proteoglycans
R-HSA-375165NCAM signaling for neurite out-growth
R-HSA-419037NCAM1 interactions
R-HSA-445144Signal transduction by L1
R-HSA-5673001RAF/MAP kinase cascade
R-HSA-877300Interferon gamma signaling
R-HSA-1266738Developmental Biology
R-HSA-1280215Cytokine Signaling in Immune system
R-HSA-1474244Extracellular matrix organization
R-HSA-162582Signal Transduction
R-HSA-168256Immune System
R-HSA-373760L1CAM interactions
R-HSA-422475Axon guidance
R-HSA-5683057MAPK family signaling cascades
R-HSA-5684996MAPK1/MAPK3 signaling
R-HSA-913531Interferon Signaling
R-HSA-9675108Nervous system development

MSigDB gene sets: 385 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, RNGTGGGC_UNKNOWN, VERHAAK_AML_WITH_NPM1_MUTATED_DN, AGGAAGC_MIR5163P, MODULE_92, BENPORATH_ES_WITH_H3K27ME3, WWTAAGGC_UNKNOWN, MODULE_274, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP, PAL_PRMT5_TARGETS_UP, GCANCTGNY_MYOD_Q6, TTTGTAG_MIR520D, GCM_ZNF198, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP

GO Biological Process (5): epithelial to mesenchymal transition (GO:0001837), cell adhesion (GO:0007155), commissural neuron axon guidance (GO:0071679), regulation of semaphorin-plexin signaling pathway (GO:2001260), symbiont entry into host cell (GO:0046718)

GO Molecular Function (2): virus receptor activity (GO:0001618), protein binding (GO:0005515)

GO Cellular Component (10): Golgi membrane (GO:0000139), extracellular region (GO:0005576), cytosol (GO:0005829), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), membrane (GO:0016020), extracellular matrix (GO:0031012), neuron projection (GO:0043005), side of membrane (GO:0098552)

Reactome top-level categories

Rollup of top-12 pathways:

CategoryPathways
Axon guidance2
Extracellular matrix organization1
NCAM signaling for neurite out-growth1
L1CAM interactions1
MAPK1/MAPK3 signaling1
Interferon Signaling1
Immune System1
Nervous system development1
Signal Transduction1
MAPK family signaling cascades1
Cytokine Signaling in Immune system1
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
membrane2
mesenchymal cell differentiation1
cellular process1
axon guidance1
regulation of signal transduction1
semaphorin-plexin signaling pathway1
viral life cycle1
symbiont entry into host1
symbiont entry into host cell1
exogenous protein binding1
binding1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
cell periphery1
plasma membrane1
cell surface1
side of membrane1
external encapsulating structure1
plasma membrane bounded cell projection1
leaflet of membrane bilayer1

Protein interactions and networks

STRING

4874 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NCAM1FCGR3AP08637990
NCAM1FCGR3BO75015990
NCAM1CD19P15391972
NCAM1CDH2P19022966
NCAM1FGFR1P11362942
NCAM1GFRA1P56159938
NCAM1CD2P06729918
NCAM1PRF1P14222916
NCAM1B3GAT1Q9P2W7915
NCAM1PRNPP04156910
NCAM1NCR3O14931908
NCAM1NCR1O76036901
NCAM1CD7P09564898
NCAM1GDNFP39905897
NCAM1NCR2O95944893

IntAct

85 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
FPR2ARL6IP5psi-mi:“MI:0914”(association)0.640
SLC39A5FAM171A2psi-mi:“MI:0914”(association)0.640
GRK2NCAM1psi-mi:“MI:0915”(physical association)0.560
STUB1NCAM1psi-mi:“MI:0915”(physical association)0.560
NUFIP1PDE2Apsi-mi:“MI:0914”(association)0.530
REEP5SCAMP1psi-mi:“MI:0914”(association)0.530
REEP1PLSCR1psi-mi:“MI:0914”(association)0.530
REEP5PLSCR1psi-mi:“MI:0914”(association)0.530
CLEC4ASEMA7Apsi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
St8sia2NCAM1psi-mi:“MI:0559”(glycosylation reaction)0.440
ST8SIA4NCAM1psi-mi:“MI:0559”(glycosylation reaction)0.440
NCAM1FGFR1psi-mi:“MI:0407”(direct interaction)0.440
NCAM1NCAM1psi-mi:“MI:0407”(direct interaction)0.440
NCAM1UCHL1psi-mi:“MI:0407”(direct interaction)0.440
SIGLEC9NCAM1psi-mi:“MI:0915”(physical association)0.400
NPTNNCAM1psi-mi:“MI:0915”(physical association)0.400
NCAM1RHEBpsi-mi:“MI:0915”(physical association)0.370
NCAM1ATXN1psi-mi:“MI:0915”(physical association)0.370
MPGRMC1psi-mi:“MI:0914”(association)0.350
PRNPWDR91psi-mi:“MI:0914”(association)0.350
FGFR4NDUFA4psi-mi:“MI:0914”(association)0.350

BioGRID (116): NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS)

ESM2 similar proteins: D3ZB51, E9PZ19, M0RAS4, O60242, O60245, O70472, O75882, O94779, P13590, P13591, P13595, P13596, P15209, P24786, P31836, P51641, P68500, P78539, P97300, P97527, P97546, Q01973, Q03351, Q15223, Q16288, Q16620, Q5IFJ9, Q5IS37, Q5IS82, Q63604, Q63769, Q6A051, Q6AZB0, Q6GQT9, Q6P1D5, Q6VNS1, Q7TNR6, Q80T74, Q80ZF8, Q8R4I7

Diamond homologs: A0A452E9Y6, A1KZ92, A2ASS6, A4IGL7, A5JUY8, A8WQH2, B0V2N1, B3A0P3, B3A0Q8, D3YXG0, G5EG78, O15146, O42414, O60469, O61213, O94779, P05164, P07202, P09933, P11247, P11678, P13591, P13595, P13596, P14650, P14781, P20241, P22063, P22079, P23468, P29533, P29534, P31836, P35419, P49290, P68500, P80025, P90820, P97528, P98160

SIGNOR signaling

3 interactions.

AEffectBMechanism
ALX4“down-regulates quantity by repression”NCAM1“transcriptional regulation”
LEF1“up-regulates activity”NCAM1“transcriptional regulation”
GDNF“up-regulates activity”NCAM1binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 103 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
NCAM signaling for neurite out-growth623.3×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

54 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance25
Likely benign2
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1098336NM_181351.5(NCAM1):c.1923dup (p.Ile642fs)Pathogenic

SpliceAI

4935 predictions. Top by Δscore:

VariantEffectΔscore
11:113040844:A:AGacceptor_gain1.0000
11:113040845:C:Gacceptor_gain1.0000
11:113133366:T:TAacceptor_gain1.0000
11:113133371:T:TAacceptor_gain1.0000
11:113133379:A:AGacceptor_gain1.0000
11:113133379:AACCT:Aacceptor_gain1.0000
11:113133380:A:Gacceptor_gain1.0000
11:113133383:T:TAacceptor_gain1.0000
11:113204284:A:AGacceptor_gain1.0000
11:113204284:AGT:Aacceptor_gain1.0000
11:113204285:G:GAacceptor_gain1.0000
11:113204285:GT:Gacceptor_gain1.0000
11:113204285:GTG:Gacceptor_gain1.0000
11:113204469:G:GGdonor_gain1.0000
11:113204500:CTTTC:Cdonor_gain1.0000
11:113204501:TTTC:Tdonor_gain1.0000
11:113204502:TTC:Tdonor_gain1.0000
11:113204502:TTCG:Tdonor_loss1.0000
11:113204503:TC:Tdonor_gain1.0000
11:113204503:TCGT:Tdonor_loss1.0000
11:113204504:CGTAA:Cdonor_loss1.0000
11:113204505:G:GGdonor_gain1.0000
11:113204505:GT:Gdonor_loss1.0000
11:113204506:T:Adonor_loss1.0000
11:113205520:CAGA:Cacceptor_loss1.0000
11:113205521:A:AGacceptor_gain1.0000
11:113205521:AG:Aacceptor_loss1.0000
11:113205522:G:GGacceptor_gain1.0000
11:113205522:GA:Gacceptor_gain1.0000
11:113205522:GAG:Gacceptor_loss1.0000

AlphaMissense

5659 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:113207373:G:CW247C1.000
11:113207373:G:TW247C1.000
11:113214473:T:AW341R1.000
11:113214473:T:CW341R1.000
11:113214475:G:CW341C1.000
11:113214475:G:TW341C1.000
11:113231694:T:CL380P1.000
11:113231732:T:GY393D1.000
11:113232271:T:AW448R1.000
11:113232271:T:CW448R1.000
11:113232273:G:CW448C1.000
11:113232273:G:TW448C1.000
11:113232350:T:CL474P1.000
11:113232771:C:AN493K1.000
11:113232771:C:GN493K1.000
11:113204320:G:CW54C0.999
11:113204320:G:TW54C0.999
11:113204400:T:CL81P0.999
11:113204438:T:GY94D0.999
11:113205627:T:AW151R0.999
11:113205627:T:CW151R0.999
11:113205629:G:CW151C0.999
11:113205629:G:TW151C0.999
11:113206073:T:CL174P0.999
11:113206111:T:GY187D0.999
11:113207371:T:AW247R0.999
11:113207371:T:CW247R0.999
11:113207372:G:CW247S0.999
11:113207901:T:CL272P0.999
11:113207939:T:GY285D0.999

dbSNP variants (sampled 300 via entrez): RS1000001757 (11:113182613 T>C), RS1000017383 (11:113270147 T>A), RS1000063052 (11:113012056 T>C), RS1000087888 (11:113194179 T>C,G), RS1000090738 (11:113263846 G>A), RS1000091760 (11:113142078 C>T), RS1000095258 (11:113222384 G>A), RS1000099720 (11:113030484 T>A,C), RS1000122924 (11:113047730 G>A), RS1000133868 (11:113240418 G>T), RS1000192230 (11:113005966 A>G), RS1000196511 (11:112962115 A>C), RS1000203201 (11:112961873 G>C), RS1000204162 (11:113160071 T>C), RS1000219898 (11:113257847 T>C,G)

Disease associations

OMIM: gene MIM:116930 | disease phenotypes:

GenCC curated gene-disease

Mondo (2): autism spectrum disorder (MONDO:0005258), hereditary breast ovarian cancer syndrome (MONDO:0003582)

Orphanet (2): Hereditary breast and/or ovarian cancer syndrome (Orphanet:145), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

50 associations (top):

StudyTraitp-value
GCST000894_3Entorhinal cortical thickness9.000000e-06
GCST000936_1Cardiac muscle measurement3.000000e-07
GCST000936_2Cardiac muscle measurement9.000000e-07
GCST000936_3Cardiac muscle measurement4.000000e-09
GCST002503_3Suicide attempts in depression or bipolar disorder2.000000e-06
GCST002783_304Body mass index1.000000e-07
GCST002783_610Body mass index2.000000e-07
GCST003174_1Sense of smell8.000000e-06
GCST003382_3Cannabis use9.000000e-07
GCST003855_17Gut microbiota (bacterial taxa)3.000000e-08
GCST006288_190Heel bone mineral density2.000000e-06
GCST006288_50Heel bone mineral density9.000000e-11
GCST006421_5Cannabis use1.000000e-10
GCST006585_1719Blood protein levels1.000000e-10
GCST006940_13Neurociticism4.000000e-12
GCST006943_13Feeling miserable1.000000e-09
GCST006944_50Experiencing mood swings9.000000e-09
GCST006952_5Feeling tense5.000000e-11
GCST006976_136Macular thickness4.000000e-08
GCST006979_421Heel bone mineral density1.000000e-23
GCST006979_422Heel bone mineral density2.000000e-42
GCST007096_227Pulse pressure3.000000e-09
GCST007099_187Systolic blood pressure4.000000e-08
GCST007323_106Risk-taking tendency (4-domain principal component model)4.000000e-24
GCST007326_110Number of sexual partners5.000000e-11
GCST007327_122Smoking status (ever vs never smokers)3.000000e-09
GCST007327_141Smoking status (ever vs never smokers)4.000000e-09
GCST007327_202Smoking status (ever vs never smokers)7.000000e-48
GCST007327_218Smoking status (ever vs never smokers)1.000000e-13
GCST007335_23Age at first sexual intercourse2.000000e-09

EFO canonical traits (27, from GWAS)

EFO IDTrait name
EFO:0004840cortical thickness
EFO:0003896left ventricular hypertrophy
EFO:0004298cardiovascular measurement
EFO:0004321attempted suicide
EFO:0004340body mass index
EFO:0007585Cannabis use
EFO:0007874gut microbiome measurement
EFO:0009270heel bone mineral density
EFO:0007660neuroticism measurement
EFO:0009598feeling miserable measurement
EFO:0008475mood instability measurement
EFO:0009596feeling tense measurement
EFO:0005763pulse pressure measurement
EFO:0006335systolic blood pressure
EFO:0008579risk-taking behaviour
EFO:0004318smoking behavior
EFO:0009749age at first sexual intercourse measurement
EFO:0005670smoking initiation
EFO:0006781coffee consumption measurement
EFO:0004337intelligence
EFO:0004784self reported educational attainment
EFO:0006527smoking status measurement
EFO:0010091tea consumption measurement
EFO:0004574total cholesterol measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0009885frailty measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D061325Hereditary Breast and Ovarian Cancer SyndromeC04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3712938 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs2303377Efficacy3duloxetineMajor Depressive Disorder

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2303377NCAM133.001duloxetine

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — CD molecules

CTD chemical–gene interactions

70 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, increases expression9
trichostatin Aaffects cotreatment, increases expression4
nickel chlorideaffects cotreatment, increases expression, increases reaction2
mercuric bromideaffects cotreatment, decreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, decreases expression, affects cotreatment2
Acetaminophenaffects expression, increases expression2
Arsenicaffects expression2
Atrazineaffects cotreatment, increases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
Tretinoinincreases expression, increases reaction, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects methylation1
O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphateaffects response to substance, affects expression1
tributyltinaffects localization, decreases reaction1
terbufosincreases methylation1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
tetrabromobisphenol Adecreases expression1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
beta-methylcholineaffects expression1
perfluorooctane sulfonic acidaffects expression1
azoxystrobindecreases expression1
hexabromocyclododecanedecreases expression1
2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-onedecreases reaction, affects localization1
corosolic acidincreases expression1
2-palmitoylglycerolincreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5318894BindingInhibition of NCAM1 transcriptional activation in human KMS-11 cells assessed as reduction in NCAM1 mRNA expression at 0.5 uM by qRT-PCR analysisStructural Modification and Pharmacological Evaluation of Substituted Quinoline-5,8-diones as Potent NSD2 Inhibitors. — J Med Chem

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1Y7Abcam HeLa NCAM1 KOCancer cell lineFemale
CVCL_B8L6Abcam HCT 116 NCAM1 KOCancer cell lineMale
CVCL_B8ZCAbcam MCF-7 NCAM1 KOCancer cell lineFemale
CVCL_B9NCAbcam A-549 NCAM1 KOCancer cell lineMale
CVCL_D1TMAbcam U-87MG NCAM1 KOCancer cell lineMale
CVCL_D9KZUbigene HEK293 NCAM1 KOTransformed cell lineFemale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT01302964PHASE3COMPLETEDMirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523PHASE3TERMINATEDOpen Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798PHASE3COMPLETEDTreatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074PHASE3COMPLETEDBehavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749PHASE3COMPLETEDA Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922PHASE3COMPLETEDTreatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917PHASE3TERMINATEDA Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875PHASE3TERMINATEDMemantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156PHASE3COMPLETEDModulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502PHASE3WITHDRAWNEfficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756PHASE3COMPLETEDOpen-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398PHASE3COMPLETEDEffect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383PHASE3TERMINATEDAmitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493PHASE3COMPLETEDThe Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707PHASE3UNKNOWNEvaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616PHASE3COMPLETEDStudy of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210PHASE3RECRUITINGSafety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hemorrhoid, irritable bowel syndrome