NCAM2

neural cell adhesion molecule 2, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 21:20998409-21543329

Links

ENSG00000154654NCBI:4685OMIM:602040HGNC:7657Uniprot:O15394AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCAM2 gene.

  • not_specified (87 variants)
  • NCAM2-related_disorder (10 variants)
  • not_provided (2 variants)
  • See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004540.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
clinvar
6
missense
85
clinvar
4
clinvar
1
clinvar
90
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 85 7 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NCAM2protein_codingprotein_codingENST00000400546 18545018
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2310.7691247740171247910.0000681
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.603444380.7850.00002205492
Missense in Polyphen84166.830.503492123
Synonymous-0.8341691561.080.000008621554
Loss of Function4.611042.40.2360.00000215554

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003670.000362
Ashkenazi Jewish0.000.00
East Asian0.00005640.0000556
Finnish0.00004680.0000464
European (Non-Finnish)0.00004860.0000441
Middle Eastern0.00005640.0000556
South Asian0.00007390.0000654
Other0.0001660.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play important roles in selective fasciculation and zone-to-zone projection of the primary olfactory axons.;
Pathway
Prion diseases - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.122

Intolerance Scores

loftool
0.378
rvis_EVS
-0.69
rvis_percentile_EVS
15.27

Haploinsufficiency Scores

pHI
0.308
hipred
Y
hipred_score
0.554
ghis
0.578

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.334

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Ncam2
Phenotype
normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); taste/olfaction phenotype; cellular phenotype;

Gene ontology

Biological process
neuron cell-cell adhesion;axonal fasciculation;sensory perception of smell
Cellular component
plasma membrane;integral component of membrane;nuclear body;axon
Molecular function
identical protein binding