EXOC3

exocyst complex component 3, the group of Exocyst complex

Basic information

Region (hg38): 5:443175-471937

Previous symbols: [ "SEC6L1" ]

Links

ENSG00000180104 ∙ NCBI:11336 ∙ OMIM:608186 ∙ HGNC:30378 ∙ Uniprot:O60645 ∙ 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 EXOC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC3 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	2
missense			64	1	1	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	64	1	3

Variants in EXOC3

This is a list of pathogenic ClinVar variants found in the EXOC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-446221-C-T		not specified	Uncertain significance (May 13, 2024)
5-446230-G-A		not specified	Uncertain significance (Jan 29, 2025)
5-446269-C-T		not specified	Uncertain significance (Jul 06, 2021)
5-446315-C-T		not specified	Uncertain significance (Oct 27, 2023)
5-446331-C-T			Benign (May 15, 2018)
5-447602-G-A		not specified	Uncertain significance (Aug 20, 2023)
5-447622-G-A			Benign (May 15, 2018)
5-447678-A-G		not specified	Uncertain significance (Mar 14, 2023)
5-447725-G-A		not specified	Uncertain significance (Jun 30, 2023)
5-453403-T-C		not specified	Uncertain significance (Nov 11, 2024)
5-453433-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-453459-C-T		not specified	Uncertain significance (Dec 21, 2023)
5-453504-A-G		not specified	Uncertain significance (Jan 30, 2024)
5-453505-C-T		not specified	Uncertain significance (May 20, 2024)
5-453541-G-A		not specified	Uncertain significance (May 21, 2024)
5-453604-T-C		not specified	Uncertain significance (Mar 03, 2025)
5-453678-C-T		not specified	Uncertain significance (Nov 10, 2024)
5-453679-G-A		not specified	Uncertain significance (Mar 07, 2024)
5-453711-G-T		not specified	Uncertain significance (Nov 10, 2022)
5-453740-G-T		not specified	Uncertain significance (Dec 16, 2024)
5-453741-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-453774-A-G		not specified	Uncertain significance (Dec 06, 2022)
5-453805-C-G		not specified	Uncertain significance (Jul 30, 2024)
5-453818-C-A		not specified	Uncertain significance (Dec 19, 2023)
5-453877-T-C		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC3	protein_coding	protein_coding	ENST00000512944	12	28780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.922	0.0778	124660	0	10	124670	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	306	452	0.678	0.0000294	4879
Missense in Polyphen		167	254.75	0.65554		2687
Synonymous	-0.586	199	189	1.05	0.0000136	1401
Loss of Function	4.25	5	30.2	0.166	0.00000128	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000491	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.
• Pathway: Arf6 trafficking events;VxPx cargo-targeting to cilium;Stabilization and expansion of the E-cadherin adherens junction;Insulin Pathway;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.371
• rvis_EVS: -1.6
• rvis_percentile_EVS: 3.04

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.714
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.818

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exoc3

Gene ontology

• Biological process: exocytosis;protein transport;exocyst localization
• Cellular component: exocyst;Golgi apparatus;cytosol;growth cone;midbody;secretory granule membrane;presynaptic membrane;perinuclear region of cytoplasm
• Molecular function: SNARE binding;protein binding;cadherin binding