GAP43

growth associated protein 43

Basic information

Region (hg38): 3:115623509-115721490

Links

ENSG00000172020 ∙ NCBI:2596 ∙ OMIM:162060 ∙ HGNC:4140 ∙ Uniprot:P17677 ∙ 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 GAP43 gene.

• Inborn genetic diseases (8 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAP43 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	1

Variants in GAP43

This is a list of pathogenic ClinVar variants found in the GAP43 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-115663790-C-T			Benign (Dec 31, 2019)
3-115663809-C-T		not specified	Uncertain significance (Jul 15, 2021)
3-115663846-G-A		not specified	Uncertain significance (May 25, 2022)
3-115663867-T-A		not specified	Likely benign (Jul 14, 2023)
3-115676026-A-T		not specified	Uncertain significance (Feb 07, 2023)
3-115676030-C-T			Likely benign (May 17, 2018)
3-115676050-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-115676166-G-C		not specified	Uncertain significance (Jan 05, 2022)
3-115676204-T-C		not specified	Likely benign (Feb 05, 2024)
3-115676374-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-115676388-G-A		not specified	Uncertain significance (Dec 21, 2022)
3-115676428-A-G		not specified	Uncertain significance (Jan 09, 2024)
3-115676460-C-A		not specified	Uncertain significance (Dec 14, 2021)
3-115676587-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAP43	protein_coding	protein_coding	ENST00000393780	3	98167

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0215	0.915	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0679	155	153	1.02	0.00000794	1782
Missense in 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

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	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Glial Cell Differentiation;Spinal Cord Injury;Developmental Biology;L1CAM interactions;Axon guidance;N-cadherin signaling events (Consensus)

Recessive Scores

• pRec: 0.354

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.536
• hipred: N
• hipred_score: 0.366
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.836

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gap43
• Phenotype: growth/size/body region phenotype; cellular 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); 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)

Gene ontology

• 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;axon regeneration;regulation of growth;tissue regeneration;cell fate commitment;regulation of filopodium assembly;regulation of postsynaptic specialization assembly
• Cellular component: cytoplasm;plasma membrane;postsynaptic density;cell junction;filopodium membrane;growth cone membrane;GABA-ergic synapse
• Molecular function: phosphatidylserine binding;protein binding;calmodulin binding;lysophosphatidic acid binding;phosphatidylinositol phosphate binding