AMN1

protein-coding

antagonist of mitotic exit network 1 homolog

Gene summary

Predicted to be involved in SCF-dependent proteasomal ubiquitin-dependent protein catabolic process. Predicted to be part of SCF ubiquitin ligase complex. Predicted to be active in microvillus membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001113402.2

Inheritance

—

ClinVar variants

U:34B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr12:31,671,142-31,729,121

External References & Databases

Ensembl (ENSG00000151743)

Transcript & Mutation Effects

hg38 • Region Span ~58.0 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 AMN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001113402.2. 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				1 clinvar		1
missense			32 clinvar	1 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	34	2	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001113402.2	RefSeq	NP_001106873.1	7	MANE Select
ENST00000281471.11	Ensembl	ENSP00000281471.6	7	MANE Select
NM_001278411.2	RefSeq	NP_001265340.1	6	Standard
NM_001278412.2	RefSeq	NP_001265341.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ubiquitin-dependent protein catabolic process
protein ubiquitination
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process

Molecular Function

ubiquitin-protein transferase activity

Cellular Component

SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281471
Coding exons: 7
Length: 58038
Individuals with no LoFs: 124602
Homozygous LoFs: 1
Heterozygous LoFs: 8
Defined: 124611
p: 0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.25	92	133	0.693	0.00000674	1653
Missense (PolyPhen)		30	41.335	0.72578		555
Synonymous	0.769	43	49.9	0.862	0.00000276	505
Loss of Function	2.54	3	12.8	0.234	6.17e-7	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00015	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.706
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.417

Gene Damage Prediction

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