AMIGO3

protein-coding

adhesion molecule with Ig like domain 3, the group of Immunoglobulin like domain containing

Gene summary

Predicted to be involved in brain development; heterophilic cell-cell adhesion; and positive regulation of synapse assembly. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_198722.3

Inheritance

—

ClinVar variants

U:93B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr3:49,716,829-49,719,684

External References & Databases

Ensembl (ENSG00000176020)

Transcript & Mutation Effects

hg38 • Region Span ~2.9 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 AMIGO3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198722.3. 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				4 clinvar		4
missense			92 clinvar	2 clinvar		94
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	6	0	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198722.3	RefSeq	NP_942015.1	1	MANE Select
ENST00000320431.8	Ensembl	ENSP00000323096.7	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
brain development
positive regulation of synapse assembly

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000535833
Coding exons: 1
Length: 7083
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125732
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0535	343	346	0.992	0.0000232	3215
Missense (PolyPhen)		85	85.271	0.99683		964
Synonymous	2.06	134	168	0.798	0.0000121	1156
Loss of Function	1.01	7	10.5	0.665	4.55e-7	112

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00020	0.00020	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May mediate heterophilic cell-cell interaction. May contribute to signal transduction through its intracellular domain (By similarity). {ECO:0000250|UniProtKB:Q80ZD5}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.692
RVIS EVS: -0.03
RVIS percentile EVS: 51.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.525

Gene Damage Prediction

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