FAT2

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

Basic information

Region (hg38): 5:151504092-151591331

Links

ENSG00000086570NCBI:2196OMIM:604269HGNC:3596Uniprot:Q9NYQ8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spinocerebellar ataxia 45ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic29053796

ClinVar

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

  • not_provided (878 variants)
  • not_specified (617 variants)
  • FAT2-related_disorder (68 variants)
  • Spinocerebellar_ataxia_45 (36 variants)
  • Cerebellar_ataxia (1 variants)
  • Spastic_ataxia (1 variants)

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. These statistics are base on transcript: NM_000001447.3. 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
4
clinvar
241
clinvar
30
clinvar
275
missense
1
clinvar
834
clinvar
135
clinvar
23
clinvar
993
nonsense
5
clinvar
5
start loss
0
frameshift
10
clinvar
10
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total 0 1 855 376 53
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FAT2protein_codingprotein_codingENST00000261800 2364852
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.02e-181.0012559301551257480.000616
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.71722922.39e+30.9590.00013328451
Missense in Polyphen757868.150.8719711021
Synonymous-1.0010239831.040.00005769010
Loss of Function6.38541340.4040.000007591582

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001240.00124
Ashkenazi Jewish0.00009920.0000992
East Asian0.0007070.000707
Finnish0.0004180.000416
European (Non-Finnish)0.0008470.000827
Middle Eastern0.0007070.000707
South Asian0.0002620.000261
Other0.0006530.000652

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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