GABARAPL1

protein-coding

GABA type A receptor associated protein like 1, the group of Autophagy related

Gene summary

Enables several functions, including Tat protein binding activity; cargo adaptor activity; and ubiquitin protein ligase binding activity. Acts upstream of or within glycophagy. Located in autophagosome and mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_031412.4

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr12:10,212,458-10,223,128

External References & Databases

Ensembl (ENSG00000139112)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 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 GABARAPL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031412.4. 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						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	0	0	10

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031412.4	RefSeq	NP_113600.1	4	MANE Select
ENST00000266458.10	Ensembl	ENSP00000266458.5	4	MANE Select
NM_001363598.2	RefSeq	NP_001350527.1	3	Standard
ENST00000421801.6	Ensembl	ENSP00000411256.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
GABAergic synapse - Homo sapiens (human)
Autophagy - animal - Homo sapiens (human)
FoxO signaling pathway - Homo sapiens (human)
Autophagy - other - Homo sapiens (human)

Biological Process

autophagosome assembly
autophagy of mitochondrion
cellular response to nitrogen starvation
macroautophagy
autophagosome maturation

Molecular Function

protein binding
Tat protein binding
ubiquitin protein ligase binding
beta-tubulin binding
GABA receptor binding

Cellular Component

autophagosome membrane
mitochondrion
autophagosome
endoplasmic reticulum
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266458
Coding exons: 4
Length: 10671
Individuals with no LoFs: 125746
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125747
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	36	62.5	0.576	0.00000291	769
Missense (PolyPhen)		13	20.396	0.63739		258
Synonymous	-0.425	26	23.4	1.11	0.00000111	201
Loss of Function	2.26	0	5.94	0.00	2.56e-7	80

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)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like modifier that increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation. {ECO:0000269|PubMed:16431922, ECO:0000269|PubMed:20404487}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.299
RVIS EVS: 0.06
RVIS percentile EVS: 58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low