AGMAT

agmatinase

Basic information

Region (hg38): 1:15571699-15585051

Links

ENSG00000116771 ∙ NCBI:79814 ∙ OMIM:617887 ∙ HGNC:18407 ∙ Uniprot:Q9BSE5 ∙ 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 AGMAT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGMAT 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	1	2
missense			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	2

Variants in AGMAT

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

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

Position	Type	Phenotype	Significance	ClinVar
1-15573657-G-A			Benign (Oct 19, 2017)
1-15573706-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-15574762-A-G		not specified	Likely benign (Jun 22, 2021)
1-15574771-G-T		not specified	Uncertain significance (Apr 26, 2023)
1-15574789-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-15574798-C-T		not specified	Uncertain significance (Mar 12, 2024)
1-15577783-C-G		not specified	Uncertain significance (Jun 18, 2021)
1-15577858-G-A		not specified	Uncertain significance (Jul 26, 2022)
1-15578893-G-A			Benign (May 30, 2017)
1-15578905-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-15578926-C-T		not specified	Uncertain significance (May 26, 2024)
1-15578959-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-15578984-G-T		not specified	Uncertain significance (Dec 28, 2022)
1-15578987-T-G		not specified	Uncertain significance (Nov 01, 2022)
1-15579005-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-15579016-G-A		not specified	Likely benign (May 08, 2024)
1-15580137-C-T		Moyamoya angiopathy	Likely pathogenic (-)
1-15583262-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-15583327-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-15583378-A-G		not specified	Uncertain significance (May 25, 2022)
1-15583384-C-T		not specified	Uncertain significance (Aug 28, 2023)
1-15583391-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-15584748-C-A		not specified	Uncertain significance (Apr 07, 2023)
1-15584773-C-A		not specified	Uncertain significance (Sep 25, 2023)
1-15584793-T-C		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGMAT	protein_coding	protein_coding	ENST00000375826	7	12758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-7	0.207	125638	0	110	125748	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.805	162	194	0.837	0.0000117	2213
Missense in Polyphen		75	91.425	0.82035		962
Synonymous	0.669	68	75.4	0.902	0.00000444	761
Loss of Function	0.200	11	11.7	0.937	5.39e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000572	0.000572
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000646	0.000642
Middle Eastern	0.000163	0.000163
South Asian	0.000425	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Arginine and proline metabolism - Homo sapiens (human);putrescine biosynthesis II;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.309
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.239

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agmat

Gene ontology

• Biological process: spermidine biosynthetic process;putrescine biosynthetic process from arginine;agmatine biosynthetic process
• Cellular component: mitochondrion
• Molecular function: agmatinase activity;metal ion binding