AGBL4

AGBL carboxypeptidase 4, the group of M14 carboxypeptidases

Basic information

Region (hg38): 1:48532854-50023954

Links

ENSG00000186094 ∙ NCBI:84871 ∙ OMIM:616476 ∙ HGNC:25892 ∙ Uniprot:Q5VU57 ∙ 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 AGBL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGBL4 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				2	1	3
missense			25		3	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding			18	2		20
Total	0	0	43	4	4

Variants in AGBL4

This is a list of pathogenic ClinVar variants found in the AGBL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-48534220-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-48534223-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-48534246-G-A		not specified	Uncertain significance (May 04, 2023)
1-48534250-G-T		not specified	Uncertain significance (Jan 10, 2023)
1-48534255-C-T		not specified	Uncertain significance (Nov 21, 2023)
1-48534893-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-48539679-C-T		AGBL4-related disorder	Benign (Mar 25, 2019)
1-48539690-C-T		not specified	Uncertain significance (Oct 05, 2021)
1-48587097-C-T		not specified	Uncertain significance (Jan 12, 2024)
1-48587118-G-C		not specified	Uncertain significance (Feb 21, 2024)
1-48587147-C-T		AGBL4-related disorder	Benign (Nov 25, 2019)
1-48587148-G-A		not specified	Uncertain significance (Mar 14, 2023)
1-48590894-C-T		not specified	Uncertain significance (May 27, 2022)
1-48590895-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-48590913-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-48590923-C-T		not specified	Uncertain significance (May 26, 2023)
1-48634513-C-A		not specified	Uncertain significance (Nov 18, 2023)
1-48653368-T-A		not specified	Uncertain significance (Feb 28, 2024)
1-48653385-T-C		not specified	Uncertain significance (Feb 08, 2023)
1-48653403-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-48653448-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-48653455-G-A		AGBL4-related disorder	Benign (Oct 28, 2019)
1-48663180-C-T		AGBL4-related disorder	Likely benign (Jul 12, 2019)
1-48663230-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-48663232-C-T		AGBL4-related disorder	Benign (Jan 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGBL4	protein_coding	protein_coding	ENST00000371839	14	1491059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000248	0.996	124612	0	30	124642	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	208	269	0.774	0.0000148	3303
Missense in Polyphen		86	119.94	0.71705		1389
Synonymous	0.887	85	96.1	0.885	0.00000490	912
Loss of Function	2.55	14	28.8	0.486	0.00000165	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000933	0.0000933
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000221
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

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 polyglutamates from the carboxy-terminus of target proteins such as MYLK. Mediates deglutamylation of CGAS, regulating the antiviral activity of CGAS. 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:Q09LZ8}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.503
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.299
• hipred: N
• hipred_score: 0.250

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agbl4
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: proteolysis;protein deglutamylation;C-terminal protein deglutamylation;protein side chain deglutamylation;defense response to virus
• Cellular component: Golgi apparatus;centriole;cytosol;ciliary basal body
• Molecular function: metallocarboxypeptidase activity;zinc ion binding;tubulin binding