EXOC3L1

protein-coding

exocyst complex component 3 like 1

Gene summary

Predicted to enable SNARE binding activity. Predicted to be involved in exocyst localization; exocytosis; and peptide hormone secretion. Predicted to be located in secretory granule. Predicted to be part of exocyst. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

EXOC3L

MANE transcript

NM_178516.4

Inheritance

—

ClinVar variants

U:122B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr16:67,184,379-67,190,185

External References & Databases

Ensembl (ENSG00000179044)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOC3L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178516.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			121 clinvar	10 clinvar		131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	122	11	0	133

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178516.4	RefSeq	NP_848611.2	13	MANE Select
ENST00000314586.11	Ensembl	ENSP00000325674.6	13	MANE Select
ENST00000545725.6	Ensembl	ENSP00000439910.2	11	Standard
ENST00000563889.1	Ensembl	ENSP00000455223.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
peptide hormone secretion
exocyst localization

Molecular Function

SNARE binding
molecular_function

Cellular Component

exocyst
transport vesicle
secretory granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314586
Coding exons: 13
Length: 5839
Individuals with no LoFs: 125623
Homozygous LoFs: 1
Heterozygous LoFs: 119
Defined: 125743
p: 0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.334	419	439	0.955	0.0000263	4620
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00072	0.00068	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00038	0.00038	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00052	0.00050	rare
South Asian	0.00066	0.00062	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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