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

ENSG00000154654 ∙ NCBI:4685 ∙ OMIM:602040 ∙ HGNC:7657 ∙ Uniprot:O15394 ∙ 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 NCAM2 gene.

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.

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				2	4	6
missense			44	3	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				4		4
Total	0	0	44	9	6

Variants in NCAM2

This is a list of pathogenic ClinVar variants found in the NCAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-20998586-A-G		not specified	Uncertain significance (Aug 26, 2024)
21-20998610-G-A		not specified	Uncertain significance (Dec 12, 2023)
21-20998611-C-T		NCAM2-related disorder	Likely benign (Jul 25, 2019)
21-21210604-C-A		NCAM2-related disorder	Likely benign (Mar 01, 2019)
21-21210643-G-A		NCAM2-related disorder	Likely benign (Mar 20, 2019)
21-21280658-T-C		NCAM2-related disorder	Benign (Jan 02, 2020)
21-21284265-G-A		not specified	Uncertain significance (Nov 26, 2024)
21-21284268-G-C		not specified	Uncertain significance (May 17, 2023)
21-21284309-T-C		NCAM2-related disorder	Likely benign (Oct 28, 2019)
21-21286292-G-A		not specified	Uncertain significance (Dec 28, 2023)
21-21286296-C-T		See cases	Uncertain significance (Jun 21, 2022)
21-21286365-C-T		not specified	Likely benign (Jul 11, 2023)
21-21286367-G-A		not specified	Uncertain significance (Aug 02, 2021)
21-21286383-A-G		not specified	Uncertain significance (Dec 14, 2023)
21-21286403-A-G		not specified	Uncertain significance (Oct 03, 2022)
21-21292104-A-G		not specified	Uncertain significance (Jun 05, 2023)
21-21292107-G-A		not specified	Uncertain significance (Jun 21, 2023)
21-21292126-C-T		NCAM2-related disorder	Benign (Apr 02, 2019)
21-21292127-A-G		not specified	Uncertain significance (Oct 26, 2022)
21-21292160-G-T		not specified	Uncertain significance (Sep 27, 2021)
21-21292196-G-A		not specified	Uncertain significance (Dec 16, 2022)
21-21292229-G-A		not specified	Uncertain significance (Mar 28, 2023)
21-21324484-G-A		not specified	Likely benign (Jun 09, 2022)
21-21324491-C-T		not specified	Uncertain significance (Mar 12, 2024)
21-21335530-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAM2	protein_coding	protein_coding	ENST00000400546	18	545018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.231	0.769	124774	0	17	124791	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	344	438	0.785	0.0000220	5492
Missense in Polyphen		84	166.83	0.50349		2123
Synonymous	-0.834	169	156	1.08	0.00000862	1554
Loss of Function	4.61	10	42.4	0.236	0.00000215	554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000564	0.0000556
Finnish	0.0000468	0.0000464
European (Non-Finnish)	0.0000486	0.0000441
Middle Eastern	0.0000564	0.0000556
South Asian	0.0000739	0.0000654
Other	0.000166	0.000165

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

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

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