EXOC3L1

exocyst complex component 3 like 1

Basic information

Region (hg38): 16:67184378-67190185

Previous symbols: [ "EXOC3L" ]

Links

ENSG00000179044 ∙ NCBI:283849 ∙ OMIM:614117 ∙ HGNC:27540 ∙ Uniprot:Q86VI1 ∙ 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 EXOC3L1 gene.

• Inborn genetic diseases (32 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC3L1 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
missense			31	4		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	5	0

Variants in EXOC3L1

This is a list of pathogenic ClinVar variants found in the EXOC3L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67184425-G-C		not specified	Uncertain significance (Jun 02, 2023)
16-67184474-G-C		not specified	Uncertain significance (Apr 25, 2022)
16-67184488-C-T			Likely benign (Jul 01, 2022)
16-67184542-G-A		not specified	Uncertain significance (Aug 10, 2023)
16-67184558-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-67184567-C-A		not specified	Uncertain significance (Jan 31, 2022)
16-67184585-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-67184714-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-67184755-A-G		not specified	Uncertain significance (Dec 28, 2023)
16-67184924-A-G		not specified	Uncertain significance (Dec 19, 2023)
16-67184952-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-67184970-C-T		not specified	Uncertain significance (Nov 08, 2022)
16-67185027-C-G		not specified	Uncertain significance (Nov 13, 2023)
16-67185042-C-T		not specified	Uncertain significance (Feb 12, 2024)
16-67185149-T-C		not specified	Uncertain significance (Sep 17, 2021)
16-67185185-G-A		not specified	Uncertain significance (Feb 12, 2024)
16-67185239-G-A		not specified	Uncertain significance (May 18, 2022)
16-67185413-A-C		not specified	Uncertain significance (Nov 09, 2023)
16-67185482-A-G		not specified	Uncertain significance (Apr 26, 2023)
16-67185489-A-G		not specified	Uncertain significance (Jun 27, 2022)
16-67186280-C-T		not specified	Uncertain significance (Jun 05, 2023)
16-67186596-T-C			Likely benign (Mar 01, 2023)
16-67186605-T-C		not specified	Likely benign (Oct 03, 2023)
16-67186609-G-T		not specified	Uncertain significance (Jan 06, 2023)
16-67186638-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC3L1	protein_coding	protein_coding	ENST00000314586	13	5839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-19	0.0224	125623	1	119	125743	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	419	439	0.955	0.0000263	4620
Missense in Polyphen		140	132.15	1.0594		1463
Synonymous	1.31	178	202	0.882	0.0000112	1681
Loss of Function	0.807	32	37.3	0.858	0.00000188	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00111
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000384	0.000381
Finnish	0.000284	0.000277
European (Non-Finnish)	0.000516	0.000501
Middle Eastern	0.000384	0.000381
South Asian	0.000658	0.000621
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the exocyst, may play a role in regulated exocytosis of insulin granules. {ECO:0000250}.

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.68

Haploinsufficiency Scores

• pHI: 0.193
• hipred: N
• hipred_score: 0.170
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exoc3l

Gene ontology

• Biological process: exocytosis;peptide hormone secretion;exocyst localization
• Cellular component: exocyst;transport vesicle;secretory granule
• Molecular function: SNARE binding;molecular_function