NCAM2

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein and may function in selective fasciculation and zone-to-zone projection of the primary olfactory axons. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004540.5

Inheritance

—

ClinVar variants

U:96B:11

Top phenotype

NCAM2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr21:20,998,409-21,543,329

External References & Databases

Ensembl (ENSG00000154654)

Transcript & Mutation Effects

hg38 • Region Span ~544.9 kb

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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 NCAM2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 95

NCAM2-related disorderTotal: 11

not providedTotal: 3

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004540.5. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	3 clinvar	7
missense			94 clinvar	3 clinvar	1 clinvar	98
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	96	7	4	107

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004540.5	RefSeq	NP_004531.2	18	MANE Select
ENST00000400546.6	Ensembl	ENSP00000383392.1	18	MANE Select
NM_001352591.2	RefSeq	NP_001339520.1	18	Standard
NM_001352592.2	RefSeq	NP_001339521.1	18	Standard

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)

Biological Process

neuron cell-cell adhesion
axonal fasciculation
sensory perception of smell

Molecular Function

identical protein binding

Cellular Component

plasma membrane
integral component of membrane
nuclear body
axon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400546
Coding exons: 18
Length: 545018
Individuals with no LoFs: 124774
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124791
p: 0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.60	344	438	0.785	0.0000220	5492
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00010	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000049	0.000044	rare
South Asian	0.000074	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play important roles in selective fasciculation and zone-to-zone projection of the primary olfactory axons.;

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.378
RVIS EVS: -0.69
RVIS percentile EVS: 15.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.334

Gene Damage Prediction

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