FAT1

FAT atypical cadherin 1, the group of Cadherin related

Basic information

Region (hg38): 4:186587793-186726722

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 (772 variants)
• Inborn genetic diseases (174 variants)
• FAT1-related condition (45 variants)
• not specified (11 variants)
• Autosomal dominant cerebellar ataxia (4 variants)
• Nephrotic syndrome (3 variants)
• Syndromic disease (2 variants)
• FAT1 related disorder (2 variants)
• Intellectual disability, moderate;Hypertensive disorder;Spasticity;Attention deficit hyperactivity disorder;Delayed speech and language development (2 variants)
• Irido-corneo-trabecular dysgenesis;Anophthalmia-microphthalmia syndrome (1 variants)
• Flexion contracture (1 variants)
• Congenital myasthenic syndrome 12 (1 variants)
• Glomerulotubular Nephropathy (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.

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			3	198	48	249
missense			423	62	37	522
nonsense	4	5	3			12
start loss						0
frameshift	2	1	1			4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4	7	1	12
non coding				47	80	127
Total	6	6	430	307	165

Highest pathogenic variant AF is 0.00000657

Variants in FAT1

This is a list of pathogenic ClinVar variants found in the FAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-186588338-C-T			Benign (Apr 03, 2020)
4-186588450-G-A			Likely benign (Mar 31, 2020)
4-186588460-G-A			Benign (Nov 12, 2018)
4-186588576-T-TG			Benign (Mar 15, 2020)
4-186588585-T-C		FAT1-related disorder	Likely benign (Mar 09, 2022)
4-186588601-C-G			Likely benign (Dec 17, 2023)
4-186588632-G-A		not specified	Benign/Likely benign (Jan 11, 2024)
4-186588637-C-T		FAT1-related disorder	Likely benign (Aug 17, 2023)
4-186588662-C-T		FAT1-related disorder	Uncertain significance (Mar 31, 2023)
4-186588684-C-T		Inborn genetic diseases	Uncertain significance (Sep 07, 2022)
4-186588687-C-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
4-186588700-G-A			Likely benign (Oct 13, 2022)
4-186588702-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
4-186588707-G-C			Benign (Dec 18, 2023)
4-186588714-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
4-186588729-C-T		Inborn genetic diseases	Uncertain significance (Mar 07, 2023)
4-186588732-T-C		FAT1-related disorder	Uncertain significance (Nov 17, 2022)
4-186588739-G-A			Likely benign (Jan 15, 2024)
4-186588752-G-C		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
4-186588765-C-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
4-186588769-G-A			Benign (Jan 12, 2024)
4-186588773-G-A		Inborn genetic diseases	Likely benign (Aug 28, 2023)
4-186588777-C-T		FAT1-related disorder	Benign/Likely benign (Jan 29, 2024)
4-186588822-T-C		Inborn genetic diseases	Uncertain significance (Mar 16, 2022)
4-186588854-T-C		Inborn genetic diseases	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAT1	protein_coding	protein_coding	ENST00000441802	26	138940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-12	1.00	124595	0	111	124706	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.431	2611	2.55e+3	1.02	0.000151	30186
Missense in Polyphen		868	965.34	0.89916		11603
Synonymous	-2.04	1129	1.05e+3	1.08	0.0000745	9126
Loss of Function	7.35	49	144	0.340	0.00000787	1900

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000902	0.000898
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000561	0.000556
Finnish	0.000279	0.000278
European (Non-Finnish)	0.000444	0.000442
Middle Eastern	0.000561	0.000556
South Asian	0.000393	0.000392
Other	0.000165	0.000165

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

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

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