AMIGO3

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

Basic information

Region (hg38): 3:49716828-49719684

Links

ENSG00000176020 ∙ NCBI:386724 ∙ OMIM:615691 ∙ HGNC:24075 ∙ Uniprot:Q86WK7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMIGO3 gene.

• Inborn genetic diseases (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMIGO3 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	1

Variants in AMIGO3

This is a list of pathogenic ClinVar variants found in the AMIGO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49717989-C-A		not specified	Uncertain significance (Nov 22, 2022)
3-49718001-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-49718006-T-C		not specified	Uncertain significance (Mar 21, 2022)
3-49718103-C-G		not specified	Uncertain significance (Oct 10, 2023)
3-49718106-C-G		not specified	Uncertain significance (Aug 02, 2022)
3-49718110-C-G		not specified	Uncertain significance (Jan 26, 2022)
3-49718209-C-CCAGCGGCGG			Benign (Jul 01, 2022)
3-49718213-C-T		not specified	Uncertain significance (Jan 20, 2023)
3-49718232-G-C		not specified	Uncertain significance (Jul 15, 2021)
3-49718244-G-C		not specified	Uncertain significance (Jun 29, 2023)
3-49718307-T-C		not specified	Uncertain significance (May 31, 2023)
3-49718425-C-T			Likely benign (Aug 01, 2022)
3-49718427-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-49718510-A-C		not specified	Uncertain significance (Jun 14, 2023)
3-49718514-G-C		not specified	Uncertain significance (May 01, 2022)
3-49718515-C-A		not specified	Uncertain significance (Feb 26, 2024)
3-49718544-G-T		not specified	Uncertain significance (Jan 18, 2022)
3-49718622-C-G		not specified	Uncertain significance (Dec 05, 2022)
3-49718653-C-G		not specified	Uncertain significance (Oct 27, 2022)
3-49718670-G-A		not specified	Uncertain significance (May 23, 2023)
3-49718696-G-A		not specified	Uncertain significance (May 15, 2023)
3-49718748-T-C		not specified	Uncertain significance (Oct 27, 2022)
3-49718943-C-G		not specified	Uncertain significance (Apr 07, 2023)
3-49719015-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-49719037-G-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMIGO3	protein_coding	protein_coding	ENST00000535833	1	7083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000208	0.747	125644	0	88	125732	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0535	343	346	0.992	0.0000232	3215
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000356	0.000352
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.000655	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0887
• hipred: N
• hipred_score: 0.272
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.525

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amigo3
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• 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