AGBL1

AGBL carboxypeptidase 1, the group of M14 carboxypeptidases|Armadillo like helical domain containing

Basic information

Region (hg38): 15:86079870-87049169

Links

ENSG00000273540 ∙ NCBI:123624 ∙ OMIM:615496 ∙ HGNC:26504 ∙ Uniprot:Q96MI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Fuchs' endothelial dystrophy (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corneal dystrophy, Fuchs endothelial, 8	AD	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	Ophthalmologic	24094747

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGBL1 gene.

• Inborn genetic diseases (52 variants)
• not provided (6 variants)
• Corneal dystrophy, Fuchs endothelial, 8 (4 variants)
• AGBL1-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGBL1 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				1		1
missense			52	4	2	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1		1	2
Total	0	0	53	5	3

Variants in AGBL1

This is a list of pathogenic ClinVar variants found in the AGBL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-86142052-G-C		AGBL1-related disorder	Benign (Jun 18, 2019)
15-86143689-T-C		AGBL1-related disorder	Likely benign (May 14, 2019)
15-86143774-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-86143816-T-C		not specified	Uncertain significance (Dec 21, 2022)
15-86143818-C-T			Likely benign (Nov 01, 2022)
15-86158938-A-C		not specified	Uncertain significance (Dec 22, 2023)
15-86158987-T-C		not specified	Uncertain significance (Nov 19, 2022)
15-86224904-C-T		AGBL1-related disorder	Benign (Mar 15, 2019)
15-86224921-A-G		not specified	Uncertain significance (Dec 14, 2023)
15-86247678-C-G		not specified	Uncertain significance (Dec 11, 2023)
15-86247682-C-T		not specified	Uncertain significance (Mar 20, 2023)
15-86247740-A-G		not specified	Uncertain significance (Jan 07, 2022)
15-86247766-G-A			Benign (Jan 01, 2024)
15-86247817-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-86247832-G-C		not specified	Uncertain significance (Jan 03, 2022)
15-86247883-G-A			Likely benign (Aug 01, 2023)
15-86256902-A-C		Corneal dystrophy, Fuchs endothelial, 8	Uncertain significance (Mar 01, 2023)
15-86256923-C-T		AGBL1-related disorder	Benign (Jul 15, 2019)
15-86256943-G-T		not specified	Uncertain significance (Aug 04, 2023)
15-86257970-T-C		not specified	Uncertain significance (Nov 10, 2022)
15-86257994-T-G		not specified	Uncertain significance (Aug 02, 2022)
15-86257996-G-T		not specified	Uncertain significance (Jan 16, 2024)
15-86258030-A-G		AGBL1-related disorder	Benign (Mar 09, 2020)
15-86262793-A-T		Corneal dystrophy, Fuchs endothelial, 8 • not specified	Uncertain significance (Dec 13, 2021)
15-86262827-T-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5. {ECO:0000250|UniProtKB:Q09M05}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Haploinsufficiency Scores

• pHI: 0.0919
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agbl1

Gene ontology

• Biological process: proteolysis;C-terminal protein deglutamylation;protein side chain deglutamylation
• Cellular component: cytosol
• Molecular function: metallocarboxypeptidase activity;zinc ion binding;tubulin binding