EXOC3L2

exocyst complex component 3 like 2, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 19:45212370-45245407

Links

ENSG00000283632

∙ NCBI:90332 ∙ OMIM:616927 ∙ HGNC:30162 ∙ Uniprot:Q2M3D2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Brain malformation renal syndrome	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; Hematologic; Neurologic; Ophthalmologic; Renal	27894351; 30327448; 34974531

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXOC3L2 gene.

not_specified (72 variants)
not_provided (48 variants)
Brain_malformation_renal_syndrome (2 variants)
EXOC3L2-related_disorder (1 variants)
Meckel-Gruber_syndrome (1 variants)
Meckel-like_syndrome (1 variants)
EXOC3L2-related_brain_malformations_and/or_renal_disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC3L2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001382422.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	12 clinvar	4 clinvar	17
missense	1 clinvar		79 clinvar	4 clinvar	3 clinvar	87
nonsense						0
start loss						0
frameshift		2 clinvar				2
splice donor/acceptor (+/-2bp)						0
Total	1	2	80	16	7

Highest pathogenic variant AF is 6.858005e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool: 0.0841
rvis_EVS: -0.16
rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

pHI: 0.106
hipred: N
hipred_score: 0.419
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Exoc3l2
Phenotype: immune system phenotype; skeleton phenotype; liver/biliary system 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); normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: exocytosis;biological_process;exocyst localization
Cellular component: exocyst;cellular_component
Molecular function: SNARE binding;molecular_function