GeneBe

FAT1

FAT atypical cadherin 1, the group of Cadherin related

Basic information

Region (hg38): 4:186587794-186726722

Previous symbols: [ "FAT" ]

Links

ENSG00000083857 ∙ NCBI:2195 ∙ OMIM:600976 ∙ HGNC:3595 ∙ Uniprot:Q14517 ∙ 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 FAT1 gene.

  • not_provided (892 variants)
  • Inborn_genetic_diseases (615 variants)
  • FAT1-related_disorder (218 variants)
  • not_specified (16 variants)
  • Nephrotic_syndrome (7 variants)
  • Autosomal_dominant_cerebellar_ataxia (7 variants)
  • Hypertensive_disorder (2 variants)
  • Intellectual_disability,_moderate (2 variants)
  • Spasticity (2 variants)
  • Attention_deficit_hyperactivity_disorder (2 variants)
  • Focal_and_Segmental_Glomerulosclerosis,_Autosomal_recessive (2 variants)
  • Delayed_speech_and_language_development (2 variants)
  • Multiple_myeloma (2 variants)
  • Syndromic_disease (2 variants)
  • Glomerulotubular_Nephropathy (1 variants)
  • Anophthalmia-microphthalmia_syndrome (1 variants)
  • Finnish_congenital_nephrotic_syndrome (1 variants)
  • Irido-corneo-trabecular_dysgenesis (1 variants)
  • Focal_segmental_glomerulosclerosis (1 variants)
  • Congenital_myasthenic_syndrome_12 (1 variants)
  • Familial_idiopathic_steroid-resistant_nephrotic_syndrome (1 variants)
  • Flexion_contracture (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005245.4. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
336
clinvar
29
clinvar
 368
missense
1
clinvar
5
clinvar
857
clinvar
126
clinvar
16
clinvar
 1005
nonsense
8
clinvar
6
clinvar
6
clinvar
 20
start loss
0
frameshift
9
clinvar
3
clinvar
6
clinvar
 18
splice donor/acceptor (+/-2bp)
1
clinvar
4
clinvar
 5
Total 18 15 876 462 45

Highest pathogenic variant AF is 0.0000495659

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FAT1protein_codingprotein_codingENST00000441802 26138940
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.20e-121.0012459501111247060.000445
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.43126112.55e+31.020.00015130186
Missense in Polyphen868965.340.8991611603
Synonymous-2.0411291.05e+31.080.00007459126
Loss of Function7.35491440.3400.000007871900

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009020.000898
Ashkenazi Jewish0.001190.00119
East Asian0.0005610.000556
Finnish0.0002790.000278
European (Non-Finnish)0.0004440.000442
Middle Eastern0.0005610.000556
South Asian0.0003930.000392
Other0.0001650.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an essential role for cellular polarization, directed cell migration and modulating cell-cell contact. {ECO:0000250}.;
Pathway
Primary Focal Segmental Glomerulosclerosis FSGS;mechanism of gene regulation by peroxisome proliferators via ppara (Consensus)

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
0.712
rvis_EVS
-0.39
rvis_percentile_EVS
27.06

Haploinsufficiency Scores

pHI
0.436
hipred
Y
hipred_score
0.593
ghis
0.507

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.652

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Fat1
Phenotype
immune system phenotype; renal/urinary system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name
fat1a
Affected structure
pronephros
Phenotype tag
abnormal
Phenotype quality
cystic

Gene ontology

Biological process
epithelial cell morphogenesis;actin filament organization;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;establishment or maintenance of cell polarity;cell-cell signaling;anatomical structure morphogenesis;cell migration;establishment or maintenance of epithelial cell apical/basal polarity;camera-type eye morphogenesis;cell-cell adhesion
Cellular component
nucleus;plasma membrane;integral component of plasma membrane;cell-cell junction;focal adhesion;apical plasma membrane;lamellipodium;filopodium;perinuclear region of cytoplasm;extracellular exosome
Molecular function
calcium ion binding;protein binding