GABARAPL3

pseudo

GABA type A receptor associated protein like 3 pseudogene

Gene summary

Predicted to enable GABA receptor binding activity; phosphatidylethanolamine binding activity; and ubiquitin protein ligase binding activity. Predicted to be involved in cellular response to nitrogen starvation and macroautophagy. Predicted to be located in autophagosome; cytoplasmic vesicle; and microtubule. Predicted to be active in autophagosome membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

N/A

Inheritance

—

ClinVar variants

—

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr15:90,348,844-90,349,197

External References & Databases

Ensembl (ENSG00000238244)

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 GABARAPL3 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Macroautophagy
Cellular responses to external stimuli

Biological Process

autophagosome assembly
autophagy of mitochondrion
cellular response to nitrogen starvation

Molecular Function

GABA receptor binding

Cellular Component

autophagosome membrane
cytosol
microtubule
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000412799
Coding exons: 1
Length: 1851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.821	46	64.6	0.712	0.00000344	758
Missense (PolyPhen)		12	19.662	0.61031		254
Synonymous	-0.518	30	26.6	1.13	0.00000151	213
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like modifier involved in autophagosome formation. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.136

Essentials

Indispensability pred.: N
Indispensability score: 0.223

Gene Damage Prediction

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