EXOC3L2

protein-coding

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

Gene summary

The protein encoded by this gene is upregulated by vascular endothelial growth factor A and interacts with exocyst complex component 4. The encoded protein may be part of an exocyst complex that plays a role in cell membrane dynamics. Mutations in this gene may be associated with Alzheimer's disease. [provided by RefSeq, May 2017]

MANE transcript

NM_001382422.1

Inheritance

ClinVar variants

P:3U:93B:32

Top phenotype

Brain malformation renal syndrome

Max pathogenic AF

—

Genomic locus

chr19:45,212,370-45,245,407

External References & Databases

Ensembl (ENSG00000283632)

Transcript & Mutation Effects

hg38 • Region Span ~33.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

brain malformation renal syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0975799

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Brain malformation renal syndromeAR

Manifestation: Craniofacial; Hematologic; Neurologic; Ophthalmologic; Renal

Intervention: General

Rationale: 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

Refs: 27894351; 30327448; 34974531

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOC3L2 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 63

Brain malformation renal syndromeTotal: 2

EXOC3L2-related disorderTotal: 1

Meckel-Gruber syndromeTotal: 1

Meckel-like syndromeTotal: 1

EXOC3L2-related brain malformations and/or renal diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382422.1. 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			4 clinvar	20 clinvar	5 clinvar	29
missense	1 clinvar		85 clinvar	4 clinvar	3 clinvar	93
nonsense			1 clinvar			1
start loss						0
frameshift		2 clinvar				2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	1	2	93	24	8	128

Highest pathogenic variant AF is 6.858005e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001382422.1	RefSeq	NP_001369351.1	11	MANE Select
ENST00000413988.3	Ensembl	ENSP00000400713.2	11	MANE Select
ENST00000857198.1	Ensembl	ENSP00000527257.1	11	Standard
ENST00000857198.2	Ensembl	ENSP00000527257.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
biological_process
exocyst localization

Molecular Function

SNARE binding
molecular_function

Cellular Component

exocyst
cellular_component

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0841
RVIS EVS: -0.16
RVIS percentile EVS: 42.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.210

Gene Damage Prediction

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