NCAM1

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

Basic information

Region (hg38): 11:112961246-113278436

Links

ENSG00000149294 ∙ NCBI:4684 ∙ OMIM:116930 ∙ HGNC:7656 ∙ Uniprot:P13591 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCAM1 gene.

• Inborn genetic diseases (11 variants)
• not provided (3 variants)
• See cases (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAM1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			10			10
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	1	0	12	1	2

Variants in NCAM1

This is a list of pathogenic ClinVar variants found in the NCAM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-112961637-T-A		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
11-113204480-G-A		not specified	Uncertain significance (May 17, 2023)
11-113207325-C-T			Benign (Aug 11, 2018)
11-113214508-A-T		not specified	Uncertain significance (Nov 03, 2022)
11-113231216-G-T		not specified	Uncertain significance (May 15, 2023)
11-113231236-G-A			Benign (Jul 01, 2022)
11-113231259-C-T		not specified	Uncertain significance (Dec 16, 2022)
11-113232175-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-113235101-G-A		not specified	Uncertain significance (Jul 20, 2021)
11-113235137-G-A		not specified	Uncertain significance (Jul 21, 2021)
11-113255966-T-TC		See cases	Pathogenic (Apr 26, 2021)
11-113260194-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-113260278-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-113260302-G-A		not specified	Uncertain significance (Jul 12, 2022)
11-113270221-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-113270223-G-C		not specified	Uncertain significance (May 27, 2022)
11-113270274-G-T		not specified	Uncertain significance (Sep 26, 2023)
11-113270325-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-113271800-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-113271850-C-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAM1	protein_coding	protein_coding	ENST00000524665	19	317162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000125	124419	0	1	124420	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.71	359	536	0.670	0.0000309	5900
Missense in Polyphen		54	177.77	0.30376		1946
Synonymous	0.163	229	232	0.986	0.0000162	1736
Loss of Function	5.98	4	49.4	0.0810	0.00000277	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a cell adhesion molecule involved in neuron-neuron adhesion, neurite fasciculation, outgrowth of neurites, etc.
• Pathway: 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;Developmental Biology;Signal Transduction;Cytokine Signaling in Immune system;Extracellular matrix organization;Immune System;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;Signal transduction by L1;Interferon gamma signaling;L1CAM interactions;NCAM1 interactions;Axon guidance;ECM proteoglycans;Interferon Signaling;FGF signaling pathway (Consensus)

Recessive Scores

• pRec: 0.885

Haploinsufficiency Scores

• pHI: 0.985
• ghis: 0.550

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.730

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ncam1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye 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); cellular phenotype

Zebrafish Information Network

• Gene name: ncam1a
• Affected structure: caudal commissure
• Phenotype tag: abnormal
• Phenotype quality: defasciculated

Gene ontology

• Biological process: MAPK cascade;cell adhesion;axon guidance;viral entry into host cell;interferon-gamma-mediated signaling pathway;commissural neuron axon guidance;regulation of semaphorin-plexin signaling pathway
• Cellular component: Golgi membrane;cytosol;plasma membrane;external side of plasma membrane;cell surface;membrane;integral component of membrane;anchored component of membrane;collagen-containing extracellular matrix
• Molecular function: virus receptor activity;Ras guanyl-nucleotide exchange factor activity