AMIGO2

protein-coding

adhesion molecule with Ig like domain 2, the group of Immunoglobulin like domain containing

Gene summary

Predicted to be involved in several processes, including heterophilic cell-cell adhesion; homophilic cell-cell adhesion; and positive regulation of synapse assembly. Predicted to be located in nucleus and plasma membrane. Predicted to be active in membrane. Biomarker of gastric adenocarcinoma. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001370299.1

Inheritance

ClinVar variants

U:65B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr12:47,075,707-47,079,959

External References & Databases

Ensembl (ENSG00000139211)

Transcript & Mutation Effects

hg38 • Region Span ~4.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

craniofacial microsomiaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0015397

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AMIGO2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370299.1. 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 clinvar	2
missense			64 clinvar	2 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	2	1	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370299.1	RefSeq	NP_001357228.1	1	MANE Select
ENST00000550413.2	Ensembl	ENSP00000449034.1	1	MANE Select
NM_001143668.1	RefSeq	NP_001137140.1	1	Standard
NM_181847.4	RefSeq	NP_862830.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway

Biological Process

homophilic cell adhesion via plasma membrane adhesion molecules
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
brain development
negative regulation of apoptotic process
negative regulation of programmed cell death

Molecular Function

protein binding

Cellular Component

nucleus
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266581
Coding exons: 1
Length: 4245
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.977	247	294	0.840	0.0000164	3434
Missense (PolyPhen)		67	102.82	0.6516		1303
Synonymous	-0.150	125	123	1.02	0.00000736	1077
Loss of Function	2.59	2	11.4	0.175	5.67e-7	160

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for depolarization-dependent survival of cultured cerebellar granule neurons. May mediate homophilic as well as heterophilic cell-cell interaction with AMIGO1 or AMIGO3. May contribute to signal transduction through its intracellular domain. May be required for tumorigenesis of a subset of gastric adenocarcinomas.;

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.160
RVIS EVS: -0.82
RVIS percentile EVS: 11.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.956

Gene Damage Prediction

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