EXOC4

exocyst complex component 4, the group of Exocyst complex|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:133253072-134067137

Previous symbols: [ "SEC8L1" ]

Links

ENSG00000131558 ∙ NCBI:60412 ∙ OMIM:608185 ∙ HGNC:30389 ∙ Uniprot:Q96A65 ∙ 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 EXOC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC4 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	3	5
missense			56	1	1	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	3	4

Variants in EXOC4

This is a list of pathogenic ClinVar variants found in the EXOC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-133253146-C-G		not specified	Uncertain significance (Dec 15, 2023)
7-133253161-C-T			Benign (May 03, 2018)
7-133253162-T-C		not specified	Uncertain significance (May 03, 2023)
7-133275028-G-T		not specified	Uncertain significance (Aug 25, 2021)
7-133275061-C-T		not specified	Uncertain significance (Jan 03, 2024)
7-133275062-G-C		not specified	Uncertain significance (Feb 16, 2023)
7-133275128-G-A		not specified	Uncertain significance (Oct 16, 2023)
7-133275139-C-T		not specified	Uncertain significance (Sep 23, 2023)
7-133288967-C-T		not specified	Uncertain significance (Sep 27, 2022)
7-133288991-A-G		not specified	Uncertain significance (Jan 05, 2022)
7-133289103-C-T		not specified	Uncertain significance (May 11, 2022)
7-133305968-T-C		not specified	Uncertain significance (Jul 21, 2021)
7-133306016-C-T		not specified	Uncertain significance (Jul 19, 2023)
7-133306037-G-A		not specified	Uncertain significance (Dec 05, 2022)
7-133317286-C-A		not specified	Uncertain significance (Dec 12, 2023)
7-133317322-T-C		not specified	Uncertain significance (Oct 03, 2023)
7-133317372-A-G		not specified	Uncertain significance (Jun 24, 2022)
7-133317375-G-A		not specified	Uncertain significance (Dec 21, 2022)
7-133356409-C-G		not specified	Uncertain significance (Apr 28, 2022)
7-133356426-C-T		not specified	Uncertain significance (Jan 26, 2023)
7-133356534-A-C		not specified	Uncertain significance (Jan 10, 2022)
7-133356540-G-C		not specified	Uncertain significance (Feb 28, 2024)
7-133356551-G-A		not specified	Uncertain significance (Feb 03, 2022)
7-133356562-G-C		not specified	Uncertain significance (Jun 12, 2023)
7-133374928-C-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC4	protein_coding	protein_coding	ENST00000253861	18	813514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.41e-13	0.994	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.516	505	539	0.937	0.0000291	6431
Missense in Polyphen		124	153.95	0.80544		1945
Synonymous	-0.162	210	207	1.01	0.0000115	1864
Loss of Function	2.70	28	48.3	0.580	0.00000267	559

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000729	0.000728
Ashkenazi Jewish	0.000210	0.000198
East Asian	0.000219	0.000217
Finnish	0.0000939	0.0000924
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.000219	0.000217
South Asian	0.000300	0.000294
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. {ECO:0000250}.
• 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)

Intolerance Scores

• loftool: 0.0710
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.17

Haploinsufficiency Scores

• pHI: 0.459
• hipred: Y
• hipred_score: 0.578
• ghis: 0.605

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exoc4
• Phenotype: hearing/vestibular/ear 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); embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein targeting to membrane;exocytosis;Golgi to plasma membrane transport;vesicle docking involved in exocytosis;chemical synaptic transmission;regulation of macroautophagy;paraxial mesoderm formation;vesicle tethering involved in exocytosis
• Cellular component: exocyst;cytoplasm;cytosol;plasma membrane;microvillus;membrane;growth cone membrane;myelin sheath abaxonal region;synapse;Flemming body
• Molecular function: protein binding;Ral GTPase binding;PDZ domain binding;protein N-terminus binding