AGMAT

protein-coding

agmatinase

Gene summary

Enables arginase activity; guanidinobutyrase activity; and guanidinopropionase activity. Predicted to be involved in putrescine biosynthetic process from arginine, via agmatine. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024758.5

Inheritance

—

ClinVar variants

P:1U:74B:6

Top phenotype

Moyamoya angiopathy

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr1:15,571,699-15,585,051

External References & Databases

Ensembl (ENSG00000116771)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGMAT variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 3

Moyamoya angiopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024758.5. 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				2 clinvar	1 clinvar	3
missense		1 clinvar	70 clinvar	2 clinvar	1 clinvar	74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	74	4	2	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024758.5	RefSeq	NP_079034.3	7	MANE Select
ENST00000375826.4	Ensembl	ENSP00000364986.3	7	MANE Select
ENST00000909207.1	Ensembl	ENSP00000579266.1	7	Standard
ENST00000909207.2	Ensembl	ENSP00000579266.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

spermidine biosynthetic process
putrescine biosynthetic process from arginine
agmatine biosynthetic process

Molecular Function

agmatinase activity
metal ion binding

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375826
Coding exons: 7
Length: 12758
Individuals with no LoFs: 125638
Homozygous LoFs: 0
Heterozygous LoFs: 110
Defined: 125748
p: 0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.805	162	194	0.837	0.0000117	2213
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00065	0.00064	rare
South Asian	0.00042	0.00042	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.213

Intolerance Scores

LoFtool: 0.309
RVIS EVS: 0.11
RVIS percentile EVS: 61.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.946

Gene Damage Prediction

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