AGBL5

AGBL carboxypeptidase 5, the group of M14 carboxypeptidases

Basic information

Region (hg38): 2:27042364-27070622

Links

ENSG00000084693

∙ NCBI:60509 ∙ OMIM:615900 ∙ HGNC:26147 ∙ Uniprot:Q8NDL9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa 75 (Strong), mode of inheritance: AR
retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 75 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 75	AR	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	26355662; 26720455

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGBL5 gene.

not_provided (621 variants)
Inborn_genetic_diseases (123 variants)
Retinal_dystrophy (74 variants)
Retinitis_pigmentosa_75 (10 variants)
AGBL5-related_disorder (7 variants)
Retinitis_pigmentosa (3 variants)
not_specified (1 variants)
Late-onset_cone-rod_dystrophy (1 variants)
Autosomal_recessive_retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGBL5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021831.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			8 clinvar	182 clinvar	6 clinvar	196
missense	1 clinvar	5 clinvar	366 clinvar	9 clinvar	3 clinvar	384
nonsense	13 clinvar		2 clinvar			15
start loss						0
frameshift	11 clinvar	5 clinvar	4 clinvar			20
splice donor/acceptor (+/-2bp)	1 clinvar	6 clinvar	5 clinvar			12
Total	26	16	385	191	9

Highest pathogenic variant AF is 0.0000173472

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGBL5	protein_coding	protein_coding	ENST00000360131	14	28259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.37e-8	1.00	125622	0	126	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	462	547	0.844	0.0000346	5753
Missense in Polyphen		101	157.29	0.64213		1502
Synonymous	-0.604	217	206	1.05	0.0000118	1874
Loss of Function	3.23	20	42.8	0.467	0.00000290	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000725	0.000719
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000498	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000318	0.000273
Middle Eastern	0.000498	0.000489
South Asian	0.00196	0.00196
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Metallocarboxypeptidase that mediates protein deglutamylation. Specifically catalyzes the deglutamylation of the branching point glutamate side chains generated by post- translational glutamylation in proteins such as tubulins. In contrast, it is not able to act as a long-chain deglutamylase that shortens long polyglutamate chains, a process catalyzed by AGTPBP1/CCP1, AGBL2/CCP2, AGBL3/CCP3, AGBL1/CCP4 and AGBL4/CCP6. Mediates deglutamylation of CGAS, regulating the antiviral activity of CGAS. {ECO:0000250|UniProtKB:Q09M02}.;
Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Intolerance Scores

loftool: 0.737
rvis_EVS: -0.99
rvis_percentile_EVS: 8.6

Haploinsufficiency Scores

pHI: 0.291
hipred: Y
hipred_score: 0.515
ghis: 0.521

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0761

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Agbl5
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); immune system phenotype;

Zebrafish Information Network

Gene name: agbl5
Affected structure: ventricular system
Phenotype tag: abnormal
Phenotype quality: edematous

Gene ontology

Biological process: proteolysis;protein deglutamylation;protein branching point deglutamylation;defense response to virus
Cellular component: nucleus;cytoplasm;cytosol;microtubule cytoskeleton;midbody;intercellular bridge;mitotic spindle
Molecular function: metallocarboxypeptidase activity;zinc ion binding;tubulin binding