EXOC1

exocyst complex component 1, the group of Exocyst complex

Basic information

Region (hg38): 4:55853647-55905086

Previous symbols: [ "SEC3L1" ]

Links

ENSG00000090989 ∙ NCBI:55763 ∙ OMIM:607879 ∙ HGNC:30380 ∙ Uniprot:Q9NV70 ∙ 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 EXOC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC1 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						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in EXOC1

This is a list of pathogenic ClinVar variants found in the EXOC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-55860453-A-G		not specified	Uncertain significance (May 04, 2023)
4-55860476-T-A		not specified	Uncertain significance (Nov 17, 2022)
4-55860504-G-A		not specified	Uncertain significance (Dec 01, 2022)
4-55864234-C-T		not specified	Uncertain significance (Jan 30, 2024)
4-55864341-C-T		not specified	Uncertain significance (Jul 13, 2021)
4-55864344-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-55864345-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-55864363-A-G		not specified	Uncertain significance (Feb 06, 2023)
4-55868434-G-A		not specified	Uncertain significance (Jun 10, 2024)
4-55868459-A-G		not specified	Likely benign (Sep 29, 2023)
4-55868459-A-T		not specified	Uncertain significance (Jan 06, 2023)
4-55868474-C-T		not specified	Uncertain significance (Jun 01, 2023)
4-55870744-G-T		not specified	Uncertain significance (Sep 20, 2023)
4-55870834-G-A		not specified	Uncertain significance (Apr 04, 2023)
4-55870868-A-G		not specified	Uncertain significance (Nov 18, 2023)
4-55871104-C-A		not specified	Uncertain significance (May 23, 2023)
4-55871170-A-G		not specified	Uncertain significance (Mar 24, 2023)
4-55871176-G-T		not specified	Uncertain significance (Jun 18, 2021)
4-55871216-A-G		not specified	Uncertain significance (May 12, 2024)
4-55871860-C-T		not specified	Uncertain significance (Apr 19, 2023)
4-55871888-G-A		not specified	Uncertain significance (Feb 22, 2023)
4-55871894-G-T		not specified	Uncertain significance (Dec 20, 2023)
4-55871903-G-A		not specified	Uncertain significance (Sep 14, 2022)
4-55871918-G-A		not specified	Uncertain significance (May 15, 2024)
4-55871954-A-C		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC1	protein_coding	protein_coding	ENST00000381295	18	51419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000690	0.999	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	335	463	0.724	0.0000232	5949
Missense in Polyphen		90	159.05	0.56586		2107
Synonymous	0.141	154	156	0.986	0.00000731	1606
Loss of Function	4.43	15	48.2	0.311	0.00000272	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000885	0.000883
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000224	0.000217
South Asian	0.000296	0.000294
Other	0.000163	0.000163

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;Insulin Pathway;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0766
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.53

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.578
• ghis: 0.617

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exoc1
• 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)

Gene ontology

• Biological process: exocytosis;Golgi to plasma membrane transport;protein transport;viral process;regulation of macroautophagy;phosphatidylinositol-mediated signaling;positive regulation of protein secretion;exocyst localization;defense response to virus
• Cellular component: exocyst;cytoplasm;cytosol;plasma membrane;membrane;perinuclear region of cytoplasm;Flemming body;cytoplasmic side of apical plasma membrane
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding;GTP-Rho binding