FERMT2
FERM domain containing kindlin 2, the group of FERM domain containing|Fermitins|Pleckstrin homology domain containing
Basic information
Region (hg38): 14:52857268-52952435
Previous symbols: [ "PLEKHC1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (62 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FERMT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006832.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 58 | 58 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FERMT2 | protein_coding | protein_coding | ENST00000343279 | 15 | 95168 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000112 | 125712 | 0 | 2 | 125714 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.96 | 258 | 363 | 0.711 | 0.0000173 | 4566 |
| Missense in Polyphen | 90 | 148.52 | 0.606 | 1899 | ||
| Synonymous | 0.250 | 122 | 126 | 0.972 | 0.00000614 | 1229 |
| Loss of Function | 5.44 | 1 | 36.4 | 0.0274 | 0.00000164 | 470 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Scaffolding protein that enhances integrin activation mediated by TLN1 and/or TLN2, but activates integrins only weakly by itself. Binds to membranes enriched in phosphoinositides. Enhances integrin-mediated cell adhesion onto the extracellular matrix and cell spreading; this requires both its ability to interact with integrins and with phospholipid membranes. Required for the assembly of focal adhesions. Participates in the connection between extracellular matrix adhesion sites and the actin cytoskeleton and also in the orchestration of actin assembly and cell shape modulation. Recruits FBLIM1 to focal adhesions. Plays a role in the TGFB1 and integrin signaling pathways. Stabilizes active CTNNB1 and plays a role in the regulation of transcription mediated by CTNNB1 and TCF7L2/TCF4 and in Wnt signaling. {ECO:0000269|PubMed:12679033, ECO:0000269|PubMed:18458155, ECO:0000269|PubMed:21325030, ECO:0000269|PubMed:22030399, ECO:0000269|PubMed:22078565, ECO:0000269|PubMed:22699938}.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.0760
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 15.2
Haploinsufficiency Scores
- pHI
- 0.864
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.642
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fermt2
- Phenotype
- limbs/digits/tail phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; 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); 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); craniofacial phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- fermt2
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- cell-matrix adhesion;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;regulation of cell shape;Wnt signaling pathway;integrin activation;cell junction assembly;substrate adhesion-dependent cell spreading;focal adhesion assembly;protein localization to membrane
- Cellular component
- stress fiber;nucleus;nucleoplasm;cytoplasm;cytosol;focal adhesion;cell cortex;cell surface;extrinsic component of cytoplasmic side of plasma membrane;lamellipodium membrane;I band
- Molecular function
- protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;actin filament binding