EXOC2

exocyst complex component 2, the group of IPT domain containing|Exocyst complex

Basic information

Region (hg38): 6:485154-693139

Previous symbols: [ "SEC5L1" ]

Links

ENSG00000112685 ∙ NCBI:55770 ∙ OMIM:615329 ∙ HGNC:24968 ∙ Uniprot:Q96KP1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with dysmorphic facies and cerebellar hypoplasia (Limited), mode of inheritance: Unknown
• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with dysmorphic facies and cerebellar hypoplasia	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	32639540

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXOC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC2 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	8	3	12
missense			42		1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			29	1	4	34
Total	0	0	72	9	8

Variants in EXOC2

This is a list of pathogenic ClinVar variants found in the EXOC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-486675-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-486719-C-T			Likely benign (Mar 01, 2022)
6-497375-C-T		not specified	Uncertain significance (May 14, 2024)
6-497455-A-G		not specified	Uncertain significance (Feb 27, 2024)
6-497478-A-G			Likely benign (Aug 01, 2023)
6-499650-C-T		not specified	Uncertain significance (Jan 31, 2023)
6-499672-C-A			Benign (Feb 13, 2018)
6-532511-A-T		not specified	Uncertain significance (Dec 03, 2021)
6-532516-C-T		not specified	Uncertain significance (Mar 04, 2024)
6-549177-G-T		not specified	Uncertain significance (Aug 12, 2021)
6-549199-G-C		not specified	Uncertain significance (Jul 14, 2021)
6-549225-C-T		EXOC2-related disorder • not specified	Uncertain significance (Apr 19, 2024)
6-549237-A-C		not specified	Uncertain significance (Nov 30, 2022)
6-549240-T-C		not specified	Uncertain significance (Feb 22, 2023)
6-549245-C-T		not specified	Uncertain significance (Dec 14, 2023)
6-549246-G-A		not specified	Uncertain significance (Oct 12, 2022)
6-553882-C-T		not specified	Uncertain significance (Apr 09, 2024)
6-555239-A-G		not specified	Uncertain significance (Mar 07, 2024)
6-555255-T-C		not specified	Uncertain significance (Jun 06, 2023)
6-555956-G-T		not specified	Uncertain significance (Jul 13, 2021)
6-555957-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-556534-A-C		not specified	Uncertain significance (Sep 29, 2023)
6-556540-C-T		not specified	Uncertain significance (Aug 16, 2021)
6-562803-T-C		not specified	Uncertain significance (Jun 28, 2022)
6-564063-C-T			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC2	protein_coding	protein_coding	ENST00000230449	27	207985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.87e-9	1.00	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	393	500	0.786	0.0000269	6071
Missense in Polyphen		133	199.52	0.66659		2374
Synonymous	-0.228	194	190	1.02	0.0000112	1709
Loss of Function	4.12	25	59.2	0.422	0.00000306	695

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.000326	0.000326

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: Ras signaling pathway - Homo sapiens (human);RalA downstream regulated genes;Chromosomal and microsatellite instability in colorectal cancer;Ras Signaling;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: 0.153

Intolerance Scores

• loftool: 0.754
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.9

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.648
• ghis: 0.611

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exoc2

Zebrafish Information Network

• Gene name: exoc2
• Affected structure: orbital region
• Phenotype tag: abnormal
• Phenotype quality: increased accumulation

Gene ontology

• Biological process: exocytosis;Golgi to plasma membrane transport;protein transport;vesicle-mediated transport;regulation of entry of bacterium into host cell
• Cellular component: exocyst;cytosol;plasma membrane;membrane;Flemming body
• Molecular function: protein binding;Ral GTPase binding;protein kinase binding;protein N-terminus binding