AGBL3

AGBL carboxypeptidase 3, the group of M14 carboxypeptidases

Basic information

Region (hg38): 7:134986507-135147963

Links

ENSG00000146856 ∙ NCBI:340351 ∙ OMIM:617346 ∙ HGNC:27981 ∙ Uniprot:Q8NEM8 ∙ 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 AGBL3 gene.

• Inborn genetic diseases (32 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGBL3 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	2	3
missense			31	2	4	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	31	3	7

Variants in AGBL3

This is a list of pathogenic ClinVar variants found in the AGBL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-134989299-C-T		not specified	Uncertain significance (Nov 12, 2021)
7-134993499-C-G			Benign (Dec 31, 2019)
7-134993502-T-C		not specified	Uncertain significance (Nov 06, 2023)
7-134993507-G-A		not specified	Uncertain significance (Dec 14, 2022)
7-134993522-C-T			Benign (Dec 11, 2018)
7-134993576-C-T			Benign (Dec 31, 2019)
7-134993588-G-A		not specified	Uncertain significance (Sep 14, 2022)
7-134993631-G-C		not specified	Uncertain significance (Oct 14, 2021)
7-134993675-A-T		not specified	Uncertain significance (Sep 29, 2023)
7-135032871-C-G		not specified	Uncertain significance (Oct 26, 2022)
7-135032877-T-C		not specified	Uncertain significance (Aug 30, 2022)
7-135032895-C-T		not specified	Uncertain significance (Jul 26, 2022)
7-135032897-T-C			Likely benign (Dec 31, 2019)
7-135034159-G-A		not specified	Uncertain significance (Apr 25, 2022)
7-135034177-C-T		not specified	Uncertain significance (Nov 12, 2021)
7-135034203-C-T			Benign (Dec 31, 2019)
7-135034207-C-A		not specified	Uncertain significance (May 09, 2023)
7-135034238-G-A		not specified	Likely benign (May 11, 2022)
7-135034304-G-T		not specified	Uncertain significance (Jun 28, 2022)
7-135034310-G-A		not specified	Uncertain significance (Aug 02, 2023)
7-135034351-A-G		not specified	Uncertain significance (Oct 04, 2022)
7-135034366-A-C		not specified	Uncertain significance (Apr 04, 2023)
7-135034379-T-G		not specified	Uncertain significance (Sep 25, 2023)
7-135034478-C-T		not specified	Uncertain significance (Mar 17, 2023)
7-135034546-C-T		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGBL3	protein_coding	protein_coding	ENST00000436302	16	161457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.18e-16	0.272	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	335	450	0.745	0.0000232	6090
Missense in Polyphen		123	169.45	0.72587		2289
Synonymous	2.28	117	153	0.765	0.00000732	1651
Loss of Function	1.38	29	38.2	0.759	0.00000217	531

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metallocarboxypeptidase that mediates both deglutamylation and deaspartylation 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 or polyaspartates from the carboxy-terminus of target proteins such as MYLK. Does not show detyrosinase or deglycylase activities from the carboxy- terminus of tubulin. {ECO:0000269|PubMed:17244817}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 1.75
• rvis_percentile_EVS: 96.67

Haploinsufficiency Scores

• pHI: 0.176

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.583

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agbl3
• Phenotype: normal phenotype

Gene ontology

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