FAT3

protein-coding

FAT atypical cadherin 3, the group of Cadherin related

Gene summary

Predicted to enable calcium ion binding activity. Predicted to be involved in cell-cell adhesion mediated by cadherin. Predicted to act upstream of or within several processes, including negative regulation of dendrite development; neuron migration; and retina layer formation. Predicted to be located in dendrite and membrane. Predicted to be active in adherens junction and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001367949.2

Inheritance

—

ClinVar variants

U:629B:111

Top phenotype

FAT3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr11:92,224,818-92,896,473

External References & Databases

Ensembl (ENSG00000165323)

Transcript & Mutation Effects

hg38 • Region Span ~671.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAT3 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 607

FAT3-related disorderTotal: 89

not providedTotal: 61

Familial meningiomaTotal: 7

EBV-positive nodal T- and NK-cell lymphomaTotal: 2

Global developmental delayTotal: 1

Hirschsprung disease, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367949.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	44 clinvar	19 clinvar	67
missense			619 clinvar	37 clinvar	11 clinvar	667
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	629	81	30	740

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367949.2	RefSeq	NP_001354878.1	27	MANE Select
ENST00000525166.6	Ensembl	ENSP00000432586.2	27	MANE Select
NM_001008781.3	RefSeq	NP_001008781.2	25	Standard
NM_001378141.1	RefSeq	NP_001365070.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
fat3a	Danio rerio	Structure: palatoquadrate cartilage Quality: disrupted abnormal

Gene / Model

Organism

Observed Phenotype

fat3a

Danio rerio

Structure: palatoquadrate cartilage

Quality: disrupted

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

homophilic cell adhesion via plasma membrane adhesion molecules
multicellular organism development

Molecular Function

calcium ion binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298047
Coding exons: 27
Length: 544357
Individuals with no LoFs: 124601
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 124663
p: 0.000249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.26	2345	2.52e+3	0.929	0.000144	30174
Missense (PolyPhen)		798	1019.6	0.78269		12657
Synonymous	-1.29	1068	1.02e+3	1.05	0.0000631	9191
Loss of Function	8.93	25	138	0.181	0.00000745	1783

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00032	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00023	0.00022	rare
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00026	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the interactions between neurites derived from specific subsets of neurons during development. {ECO:0000250}.;

Essentials

Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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