FLRT2
fibronectin leucine rich transmembrane protein 2, the group of Fibronectin type III domain containing
Basic information
Region (hg38): 14:85530144-85654428
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (73 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FLRT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013231.6. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 73 | 74 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 73 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FLRT2 | protein_coding | protein_coding | ENST00000330753 | 1 | 98547 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.817 | 0.183 | 125725 | 0 | 4 | 125729 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 314 | 384 | 0.817 | 0.0000237 | 4309 |
| Missense in Polyphen | 57 | 120.5 | 0.47301 | 1401 | ||
| Synonymous | -1.70 | 189 | 161 | 1.17 | 0.0000103 | 1361 |
| Loss of Function | 3.37 | 3 | 18.8 | 0.160 | 0.00000112 | 203 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in cell-cell adhesion, cell migration and axon guidance. Mediates cell-cell adhesion via its interactions with ADGRL3 and probably also other latrophilins that are expressed at the surface of adjacent cells. May play a role in the migration of cortical neurons during brain development via its interaction with UNC5D. Mediates axon growth cone collapse and plays a repulsive role in neuron guidance via its interaction with UNC5D, and possibly also other UNC-5 family members. Plays a role in fibroblast growth factor-mediated signaling cascades. Required for normal organization of the cardiac basement membrane during embryogenesis, and for normal embryonic epicardium and heart morphogenesis. {ECO:0000250|UniProtKB:Q8BLU0}.;
- Pathway
- Signal Transduction;Signaling by FGFR;Signaling by Receptor Tyrosine Kinases;Downstream signaling of activated FGFR1;Signaling by FGFR1
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- rvis_EVS
- -0.04
- rvis_percentile_EVS
- 50.45
Haploinsufficiency Scores
- pHI
- 0.224
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.537
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Flrt2
- 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); 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); 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- heart morphogenesis;axon guidance;biological_process;fibroblast growth factor receptor signaling pathway;negative chemotaxis;positive regulation of synapse assembly;cell adhesion involved in heart morphogenesis;basement membrane organization;regulation of neuron migration
- Cellular component
- endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;cell-cell junction;focal adhesion;extracellular matrix;organelle membrane;neuron projection;synapse;extracellular exosome
- Molecular function
- fibroblast growth factor receptor binding;protein binding, bridging;chemorepellent activity