NCAM1

protein-coding

neural cell adhesion molecule 1, the group of CD molecules|Ig-like cell adhesion molecule family|Fibronectin type III domain containing|I-set domain containing

Gene summary

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. [provided by RefSeq, Aug 2020]

MANE transcript

NM_181351.5

Inheritance

—

ClinVar variants

P:2U:33B:3

Top phenotype

Ruzayqat's NCAM1 Related Neurological Disorders

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr11:112,961,275-113,278,436

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~317.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NCAM1 variants in ClinVar

6 Conditions Cataloged
not specifiedTotal: 22
not providedTotal: 6
Ruzayqat's NCAM1 Related Neurological DisordersTotal: 1
Hereditary breast ovarian cancer syndromeTotal: 1
Autism spectrum disorderTotal: 1
See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181351.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
1
clinvar
4
missense
1
clinvar
26
clinvar
27
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total11332138

Highest pathogenic variant AF is 0.00001664213

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_181351.5RefSeqNP_851996.220MANE Select
ENST00000316851.12EnsemblENSP00000318472.820MANE Select
NM_000615.7RefSeqNP_000606.319Standard
NM_001076682.4RefSeqNP_001070150.120Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ncam1aDanio rerio

Structure: caudal commissure

Quality: defasciculated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Prion diseases - Homo sapiens (human)
  • Cell adhesion molecules (CAMs) - Homo sapiens (human)
  • Brain-Derived Neurotrophic Factor (BDNF) signaling pathway
  • Cardiac Progenitor Differentiation
  • Prion disease pathway

Biological Process

  • MAPK cascade
  • cell adhesion
  • axon guidance
  • viral entry into host cell
  • interferon-gamma-mediated signaling pathway

Molecular Function

  • virus receptor activity
  • Ras guanyl-nucleotide exchange factor activity

Cellular Component

  • Golgi membrane
  • cytosol
  • plasma membrane
  • external side of plasma membrane
  • cell surface

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000524665
Coding exons
19
Length
317162
Individuals with no LoFs
124419
Homozygous LoFs
0
Heterozygous LoFs
1
Defined
124420
p
0.00000402
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.713595360.6700.00003095900
Missense (PolyPhen)54177.770.303761946
Synonymous0.1632292320.9860.00001621736
Loss of Function5.98449.40.08100.00000277525

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: This protein is a cell adhesion molecule involved in neuron-neuron adhesion, neurite fasciculation, outgrowth of neurites, etc.;

Recessive Scores

pRec
0.885

Essentials

Essential (CRISPR2)
N
Indispensability pred.
E
Indispensability score
0.730

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.