GABARAPL3

GABA type A receptor associated protein like 3 pseudogene

Basic information

Region (hg38): 15:90348844-90349197

Links

ENSG00000238244 ∙ NCBI:23766 ∙ ∙ HGNC:4069 ∙ Uniprot:Q9BY60 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GABARAPL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABARAPL3 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABARAPL3	protein_coding	protein_coding	ENST00000412799	1	1851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

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}.
• Pathway: Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.136

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.171
• ghis: 0.395

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation
• Cellular component: autophagosome membrane;cytosol;microtubule;cytoplasmic vesicle
• Molecular function: GABA receptor binding