FAT2

FAT atypical cadherin 2, the group of Cadherin related|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:151504092-151591331

Links

ENSG00000086570 ∙ NCBI:2196 ∙ OMIM:604269 ∙ HGNC:3596 ∙ Uniprot:Q9NYQ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia 45 (Limited), mode of inheritance: AD
• spinocerebellar ataxia 45 (Supportive), mode of inheritance: AD
• spinocerebellar ataxia 45 (Limited), mode of inheritance: AD
• spinocerebellar ataxia 45 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 45	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29053796

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAT2 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	210	51	264
missense		1	530	67	39	637
nonsense			4			4
start loss						0
frameshift			8			8
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			4	5	2	11
non coding			1	14	44	59
Total	0	1	547	291	134

Variants in FAT2

This is a list of pathogenic ClinVar variants found in the FAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151505573-T-C		not specified	Uncertain significance (Jun 29, 2023)
5-151505584-C-T		FAT2-related disorder	Likely benign (Apr 07, 2018)
5-151505612-C-T		not specified	Uncertain significance (Jul 19, 2022)
5-151505620-T-C			Uncertain significance (Nov 08, 2022)
5-151505626-T-C			Uncertain significance (Oct 13, 2023)
5-151505646-G-C			Likely benign (Jul 01, 2022)
5-151505656-G-A		not specified	Uncertain significance (Jul 26, 2021)
5-151505657-C-T		not specified	Likely benign (Jul 26, 2021)
5-151505674-A-T		not specified	Uncertain significance (Jul 05, 2023)
5-151505678-CACAG-C		not specified	Uncertain significance (Dec 08, 2022)
5-151505702-C-T		not specified	Conflicting classifications of pathogenicity (May 01, 2024)
5-151505704-C-T			Uncertain significance (May 21, 2022)
5-151505705-G-A			Uncertain significance (Apr 10, 2022)
5-151505713-C-T		not specified	Uncertain significance (Oct 27, 2023)
5-151505714-G-C			Uncertain significance (Sep 28, 2023)
5-151505716-A-G		Spinocerebellar ataxia 45	Uncertain significance (Jul 22, 2021)
5-151505723-C-A		not specified	Uncertain significance (Oct 12, 2024)
5-151505734-C-A		not specified	Uncertain significance (Nov 15, 2022)
5-151505738-C-T			Uncertain significance (Jun 14, 2023)
5-151505749-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-151505753-GC-TT			Uncertain significance (Oct 17, 2022)
5-151505761-C-A		not specified	Uncertain significance (May 23, 2023)
5-151505761-C-G		FAT2-related disorder	Likely benign (Dec 22, 2023)
5-151505762-C-G			Likely benign (Jan 01, 2023)
5-151505762-C-T		not specified	Uncertain significance (Sep 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAT2	protein_coding	protein_coding	ENST00000261800	23	64852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.02e-18	1.00	125593	0	155	125748	0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.717	2292	2.39e+3	0.959	0.000133	28451
Missense in Polyphen		757	868.15	0.87197		11021
Synonymous	-1.00	1023	983	1.04	0.0000576	9010
Loss of Function	6.38	54	134	0.404	0.00000759	1582

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000707	0.000707
Finnish	0.000418	0.000416
European (Non-Finnish)	0.000847	0.000827
Middle Eastern	0.000707	0.000707
South Asian	0.000262	0.000261
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of cell migration (PubMed:18534823). May be involved in mediating the organization of the parallel fibers of granule cells during cerebellar development (By similarity). {ECO:0000250|UniProtKB:O88277, ECO:0000269|PubMed:18534823}.

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.642
• rvis_EVS: 1.95
• rvis_percentile_EVS: 97.53

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.492
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fat2
• Phenotype: normal phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;epithelial cell migration;cell-substrate adhesion
• Cellular component: Golgi apparatus;plasma membrane;cell-cell adherens junction;integral component of membrane;extracellular exosome
• Molecular function: calcium ion binding