AMOTL1

angiomotin like 1

Basic information

Region (hg38): 11:94706431-94876748

Links

ENSG00000166025

∙ NCBI:154810 ∙ OMIM:614657 ∙ HGNC:17811 ∙ Uniprot:Q8IY63 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

orofacial cleft (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMOTL1 gene.

not_specified (123 variants)
not_provided (20 variants)
CRANIOFACIOCARDIOHEPATIC_SYNDROME (5 variants)
AMOTL1-associated_disorder (2 variants)
Long_fingers (1 variants)
Cleft_lip/palate (1 variants)
Tethered_cord (1 variants)
Abnormal_pinna_morphology (1 variants)
Hypertelorism (1 variants)
imperforate_anus_with_fistula (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMOTL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130847.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	6 clinvar	8
missense	4 clinvar	2 clinvar	128 clinvar	2 clinvar		136
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	2	130	4	6

Highest pathogenic variant AF is 0.0000056426

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMOTL1	protein_coding	protein_coding	ENST00000433060	13	170322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00183	0.998	124655	0	31	124686	0.000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	471	552	0.854	0.0000323	6193
Missense in Polyphen		206	254.17	0.81047		2735
Synonymous	0.301	221	227	0.975	0.0000141	1882
Loss of Function	4.41	14	46.4	0.301	0.00000273	487

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.000298	0.000278
Finnish	0.000101	0.0000928
European (Non-Finnish)	0.000117	0.000115
Middle Eastern	0.000298	0.000278
South Asian	0.0000657	0.0000654
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

Function: FUNCTION: Inhibits the Wnt/beta-catenin signaling pathway, probably by recruiting CTNNB1 to recycling endosomes and hence preventing its translocation to the nucleus. {ECO:0000269|PubMed:22362771}.;
Pathway: Tight junction - Homo sapiens (human);Signal Transduction;Signaling by Hippo (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.671
rvis_EVS: -0.44
rvis_percentile_EVS: 24.68

Haploinsufficiency Scores

pHI: 0.327
hipred: Y
hipred_score: 0.701
ghis: 0.533

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Amotl1
Phenotype

Zebrafish Information Network

Gene name: amotl1
Affected structure: intersegmental vessel
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: angiogenesis;establishment of cell polarity involved in ameboidal cell migration;Wnt signaling pathway;actin cytoskeleton organization;regulation of cell migration;hippo signaling;positive regulation of blood vessel endothelial cell migration
Cellular component: cytosol;bicellular tight junction;COP9 signalosome;apical plasma membrane;lamellipodium;cytoplasmic vesicle
Molecular function: protein binding;identical protein binding