GAP43

protein-coding

growth associated protein 43

Gene summary

The protein encoded by this gene has been termed a 'growth' or 'plasticity' protein because it is expressed at high levels in neuronal growth cones during development and axonal regeneration. This protein is considered a crucial component of an effective regenerative response in the nervous system. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002045.4

Inheritance

—

ClinVar variants

U:38B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr3:115,623,510-115,721,490

External References & Databases

Ensembl (ENSG00000172020)

Transcript & Mutation Effects

hg38 • Region Span ~98.0 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 GAP43 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002045.4. 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				3 clinvar		3
missense			37 clinvar			37
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	3	0	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002045.4	RefSeq	NP_002036.1	3	MANE Select
ENST00000305124.11	Ensembl	ENSP00000305010.7	3	MANE Select
NM_001130064.2	RefSeq	NP_001123536.1	3	Standard
ENST00000393780.3	Ensembl	ENSP00000377372.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glial Cell Differentiation
Spinal Cord Injury
Developmental Biology
L1CAM interactions
Axon guidance

Biological Process

protein kinase C-activating G protein-coupled receptor signaling pathway
nervous system development
response to wounding
glial cell differentiation
axon choice point recognition

Molecular Function

phosphatidylserine binding
protein binding
calmodulin binding
lysophosphatidic acid binding
phosphatidylinositol phosphate binding

Cellular Component

cytoplasm
plasma membrane
postsynaptic density
cell junction
filopodium membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393780
Coding exons: 3
Length: 98167
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0679	155	153	1.02	0.00000794	1782
Missense (PolyPhen)		56	57.002	0.98243		665
Synonymous	-0.100	63	62.0	1.02	0.00000392	548
Loss of Function	1.58	4	9.16	0.437	4.49e-7	124

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: This protein is associated with nerve growth. It is a major component of the motile "growth cones" that form the tips of elongating axons. Plays a role in axonal and dendritic filopodia induction. {ECO:0000269|PubMed:14978216, ECO:0000269|PubMed:21152083}.;

Recessive Scores

pRec: 0.354

Intolerance Scores

LoFtool: 0.332
RVIS EVS: -0.45
RVIS percentile EVS: 24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.836

Gene Damage Prediction

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