FAT3

FAT atypical cadherin 3, the group of Cadherin related

Basic information

Region (hg38): 11:92224817-92896473

Links

ENSG00000165323 ∙ NCBI:120114 ∙ OMIM:612483 ∙ HGNC:23112 ∙ Uniprot:Q8TDW7 ∙ 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 FAT3 gene.

• Inborn genetic diseases (166 variants)
• not provided (52 variants)
• FAT3-related condition (2 variants)
• Global developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAT3 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				20	11	31
missense			171	9	7	187
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	171	29	18

Variants in FAT3

This is a list of pathogenic ClinVar variants found in the FAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-92352191-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-92352204-A-C		not specified	Uncertain significance (Feb 26, 2024)
11-92352250-C-A		FAT3-related disorder	Likely benign (Sep 24, 2019)
11-92352381-G-C		not specified	Uncertain significance (May 26, 2022)
11-92352397-G-C		not specified	Uncertain significance (Jul 14, 2021)
11-92352457-C-T		FAT3-related disorder	Likely benign (Mar 01, 2023)
11-92352563-A-G		not specified	Uncertain significance (Aug 10, 2023)
11-92352664-C-T		FAT3-related disorder	Likely benign (May 28, 2019)
11-92352765-G-A		not specified	Uncertain significance (Jun 16, 2023)
11-92352832-G-T		FAT3-related disorder	Likely benign (Dec 24, 2019)
11-92352921-C-T		not specified	Uncertain significance (Oct 26, 2021)
11-92353179-G-A		FAT3-related disorder	Benign (May 28, 2019)
11-92353203-T-C		Global developmental delay	Uncertain significance (Jan 04, 2022)
11-92353265-A-G		not specified	Likely benign (Sep 01, 2021)
11-92353292-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-92353306-A-C		FAT3-related disorder	Likely benign (Dec 18, 2019)
11-92353347-C-T		FAT3-related disorder	Benign (Dec 09, 2019)
11-92353352-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-92353483-G-A		FAT3-related disorder	Benign (Dec 09, 2019)
11-92353582-C-T		FAT3-related disorder	Likely benign (Apr 25, 2019)
11-92353583-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-92353619-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-92353662-T-C		FAT3-related disorder	Benign/Likely benign (Jun 01, 2023)
11-92353776-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-92353781-C-T		not specified	Uncertain significance (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAT3	protein_coding	protein_coding	ENST00000298047	27	544357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000498	124601	0	62	124663	0.000249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	2345	2.52e+3	0.929	0.000144	30174
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000586	0.000584
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000226	0.000223
Finnish	0.000188	0.000186
European (Non-Finnish)	0.000242	0.000239
Middle Eastern	0.000226	0.000223
South Asian	0.000263	0.000261
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.466
• ghis: 0.519

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fat3
• 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

Zebrafish Information Network

• Gene name: fat3a
• Affected structure: palatoquadrate cartilage
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;multicellular organism development
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: calcium ion binding