AMIGO1

adhesion molecule with Ig like domain 1, the group of V-set domain containing

Basic information

Region (hg38): 1:109504177-109509738

Links

ENSG00000181754 ∙ NCBI:57463 ∙ OMIM:615689 ∙ HGNC:20824 ∙ Uniprot:Q86WK6 ∙ 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 AMIGO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMIGO1 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						0
missense			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	1

Variants in AMIGO1

This is a list of pathogenic ClinVar variants found in the AMIGO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109507489-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-109507531-T-A		not specified	Uncertain significance (Dec 27, 2023)
1-109507594-C-T		not specified	Uncertain significance (Nov 08, 2021)
1-109507649-T-A		not specified	Uncertain significance (Aug 28, 2023)
1-109507681-C-G		not specified	Uncertain significance (Sep 01, 2021)
1-109507703-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-109507708-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-109507718-A-G		not specified	Uncertain significance (Mar 23, 2022)
1-109507772-T-C		not specified	Uncertain significance (Aug 16, 2021)
1-109507992-T-G		not specified	Uncertain significance (Dec 09, 2023)
1-109508006-T-C		not specified	Uncertain significance (Jul 05, 2023)
1-109508086-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-109508143-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-109508305-G-A		not specified	Uncertain significance (Apr 25, 2022)
1-109508363-G-C		not specified	Uncertain significance (Jun 01, 2023)
1-109508371-C-T		not specified	Uncertain significance (Jun 04, 2024)
1-109508590-G-A		not specified	Uncertain significance (Nov 13, 2023)
1-109508665-G-C		not specified	Uncertain significance (Jan 23, 2024)
1-109508831-C-T		not specified	Uncertain significance (Oct 30, 2023)
1-109508840-C-T			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMIGO1	protein_coding	protein_coding	ENST00000369864	1	5564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0159	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	149	285	0.524	0.0000170	3214
Missense in Polyphen		29	107.05	0.27089		1258
Synonymous	1.53	106	128	0.828	0.00000763	1044
Loss of Function	3.29	0	12.6	0.00	6.31e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes growth and fasciculation of neurites from cultured hippocampal neurons. May be involved in fasciculation as well as myelination of developing neural axons. May have a role in regeneration as well as neural plasticity in the adult nervous system. May mediate homophilic as well as heterophilic cell-cell interaction and contribute to signal transduction through its intracellular domain. Assembled with KCNB1 modulates the gating characteristics of the delayed rectifier voltage-dependent potassium channel KCNB1. {ECO:0000250|UniProtKB:Q80ZD7, ECO:0000250|UniProtKB:Q80ZD8}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.276
• hipred: Y
• hipred_score: 0.707
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amigo1

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;axonogenesis;axonal fasciculation;brain development;myelination;positive regulation of axonogenesis;positive regulation of synapse assembly;positive regulation of potassium ion transmembrane transport
• Cellular component: voltage-gated potassium channel complex;integral component of membrane;axon;dendrite;neuronal cell body membrane;perikaryon
• Molecular function: potassium channel regulator activity