AGBL2

protein-coding

AGBL carboxypeptidase 2, the group of M14 carboxypeptidases

Gene summary

Predicted to enable metallocarboxypeptidase activity and tubulin binding activity. Predicted to be involved in protein side chain deglutamylation. Located in centriole and ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024783.4

Inheritance

ClinVar variants

P:1U:100B:13

Top phenotype

Epilepsy

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr11:47,659,591-47,715,389

External References & Databases

Ensembl (ENSG00000165923)

Transcript & Mutation Effects

hg38 • Region Span ~55.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epilepsyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005027

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGBL2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 9

EpilepsyTotal: 1

Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024783.4. 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			1 clinvar		3 clinvar	4
missense			94 clinvar	8 clinvar	1 clinvar	103
nonsense		1 clinvar	2 clinvar			3
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	1	100	8	5	114

Highest pathogenic variant AF is 0.000016730262

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024783.4	RefSeq	NP_079059.2	18	MANE Select
ENST00000525123.6	Ensembl	ENSP00000435582.1	18	MANE Select
ENST00000528244.5	Ensembl	ENSP00000436630.1	15	Standard
ENST00000528609.5	Ensembl	ENSP00000431912.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Carboxyterminal post-translational modifications of tubulin

Biological Process

proteolysis
protein side chain deglutamylation

Molecular Function

metallocarboxypeptidase activity
zinc ion binding

Cellular Component

centriole
cytosol
ciliary basal body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000525123
Coding exons: 18
Length: 55799
Individuals with no LoFs: 125351
Homozygous LoFs: 1
Heterozygous LoFs: 395
Defined: 125747
p: 0.00158

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	390	461	0.846	0.0000229	5952
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0054	0.0054	notable
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.0084	0.0084	notable
Finnish	0.00056	0.00055	rare
European (Non-Finnish)	0.00078	0.00078	rare
South Asian	0.00079	0.00078	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.952
RVIS EVS: 0.36
RVIS percentile EVS: 74.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.506

Gene Damage Prediction

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