AGBL2

AGBL carboxypeptidase 2, the group of M14 carboxypeptidases

Basic information

Region (hg38): 11:47659591-47715389

Links

ENSG00000165923 ∙ NCBI:79841 ∙ OMIM:617345 ∙ HGNC:26296 ∙ Uniprot:Q5U5Z8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGBL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGBL2 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					3	3
missense			29	5	1	35
nonsense		1	1			2
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	1	30	6	5

Variants in AGBL2

This is a list of pathogenic ClinVar variants found in the AGBL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47660176-C-T			Benign (Dec 31, 2019)
11-47660194-C-G		not specified	Uncertain significance (Nov 27, 2023)
11-47660204-T-C		not specified	Uncertain significance (Nov 22, 2022)
11-47660210-G-A			Likely benign (Jan 19, 2018)
11-47660259-A-C		not specified	Uncertain significance (Dec 15, 2023)
11-47660299-T-C		not specified	Uncertain significance (Jan 26, 2022)
11-47660326-T-C			Benign (Dec 31, 2019)
11-47667023-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-47667662-T-A		not specified	Uncertain significance (Dec 16, 2022)
11-47668896-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-47677261-T-C			Likely benign (Mar 30, 2018)
11-47677295-A-T		not specified	Uncertain significance (Nov 30, 2021)
11-47677371-G-A		not specified	Uncertain significance (Apr 28, 2023)
11-47680038-G-C		not specified	Uncertain significance (Oct 02, 2023)
11-47685934-G-A		Abnormal brain morphology	Likely pathogenic (-)
11-47685954-C-T		not specified	Uncertain significance (Sep 20, 2023)
11-47690085-A-G		not specified	Uncertain significance (Jul 11, 2023)
11-47690112-A-T		not specified	Uncertain significance (Jul 19, 2022)
11-47690158-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-47690175-T-A		not specified	Uncertain significance (Jun 11, 2024)
11-47690227-CA-C			Benign (Dec 11, 2018)
11-47690232-A-G		not specified	Uncertain significance (Nov 14, 2023)
11-47690296-C-T		not specified	Likely benign (Oct 26, 2021)
11-47690350-T-G		not specified	Uncertain significance (Feb 16, 2023)
11-47690399-C-A		not specified	Uncertain significance (Jan 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGBL2	protein_coding	protein_coding	ENST00000525123	18	55799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.96e-16	0.885	125351	1	395	125747	0.00158

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	390	461	0.846	0.0000229	5952
Missense in Polyphen		126	147.39	0.85486		1874
Synonymous	0.123	163	165	0.988	0.00000805	1644
Loss of Function	2.16	32	48.2	0.665	0.00000270	582

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00579	0.00580
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.00843	0.00841
Finnish	0.000557	0.000554
European (Non-Finnish)	0.000785	0.000783
Middle Eastern	0.00843	0.00841
South Asian	0.000788	0.000784
Other	0.00131	0.00130

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. Does not show detyrosinase or deglycylase activities from the carboxy-terminus of tubulin. {ECO:0000250|UniProtKB:Q8CDK2, ECO:0000269|PubMed:21303978}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Intolerance Scores

• loftool: 0.952
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.68

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.169
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agbl2
• Phenotype: normal phenotype

Gene ontology

• Biological process: proteolysis;protein side chain deglutamylation
• Cellular component: centriole;cytosol;ciliary basal body
• Molecular function: metallocarboxypeptidase activity;zinc ion binding