AMIGO2

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

Basic information

Region (hg38): 12:47075706-47079959

Links

ENSG00000139211 ∙ NCBI:347902 ∙ OMIM:615690 ∙ HGNC:24073 ∙ Uniprot:Q86SJ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• craniofacial microsomia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMIGO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMIGO2 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
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	1

Variants in AMIGO2

This is a list of pathogenic ClinVar variants found in the AMIGO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-47077487-A-G		not specified	Uncertain significance (Nov 04, 2022)
12-47077496-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-47077521-C-T			Benign (Dec 31, 2019)
12-47077622-C-T		not specified	Uncertain significance (Nov 19, 2022)
12-47077642-G-T		not specified	Uncertain significance (Jun 05, 2023)
12-47077714-C-G		not specified	Uncertain significance (Dec 21, 2023)
12-47077736-G-A		not specified	Uncertain significance (May 05, 2023)
12-47077840-C-T		not specified	Likely benign (Mar 15, 2024)
12-47077894-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-47077895-G-T		not specified	Uncertain significance (Dec 14, 2023)
12-47077906-A-G		not specified	Uncertain significance (Jul 19, 2023)
12-47077915-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-47077985-A-G		not specified	Uncertain significance (Mar 29, 2022)
12-47077994-T-A		not specified	Uncertain significance (Oct 05, 2023)
12-47078020-T-C		not specified	Uncertain significance (Jan 16, 2024)
12-47078021-T-C		not specified	Uncertain significance (Oct 05, 2023)
12-47078033-C-T		not specified	Likely benign (Oct 17, 2023)
12-47078105-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-47078106-C-A		not specified	Uncertain significance (Dec 21, 2022)
12-47078134-G-T		not specified	Uncertain significance (Aug 28, 2023)
12-47078174-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-47078222-G-T		not specified	Uncertain significance (Sep 14, 2022)
12-47078269-C-G		not specified	Uncertain significance (Oct 25, 2023)
12-47078345-G-C		not specified	Uncertain significance (Jul 11, 2023)
12-47078396-G-C		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMIGO2	protein_coding	protein_coding	ENST00000266581	1	4245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.597	0.401	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.977	247	294	0.840	0.0000164	3434
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.160
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.545
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amigo2

Gene ontology

• 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;positive regulation of synapse assembly
• Cellular component: nucleus;plasma membrane;integral component of membrane
• Molecular function: protein binding