FRMD3
protein-codingFERM domain containing 3, the group of FERM domain containing
Gene summary
The protein encoded by this gene is a single pass membrane protein primarily found in ovaries. A similar protein in erythrocytes helps determine the shape of red blood cells, but the function of the encoded protein has not been determined. There is some evidence that this is a tumor suppressor gene, and there is also evidence linking defects in this gene to susceptibility to diabetic nephropathy in type 1 diabetes. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~295.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FRMD3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_174938.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 74 | 74 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 78 | 1 | 0 | 79 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_777598.3 | 14 | MANE Select | |
| Ensembl | ENSP00000303508.3 | 14 | MANE Select | |
| RefSeq | NP_001231888.1 | 15 | Standard | |
| RefSeq | NP_001231889.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- actomyosin structure organization
Molecular Function
- cytoskeletal protein binding
Cellular Component
- cytoskeleton
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000304195
- Coding exons
- 14
- Length
- 295557
- Individuals with no LoFs
- 124765
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 31
- Defined
- 124796
- p
- 0.000124
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.879 | 267 | 311 | 0.860 | 0.0000151 | 3941 |
| Missense (PolyPhen) | 75 | 98.651 | 0.76025 | 1284 | ||
| Synonymous | -2.01 | 143 | 115 | 1.24 | 0.00000574 | 1102 |
| Loss of Function | 3.87 | 7 | 29.8 | 0.235 | 0.00000133 | 395 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.0014 | 0.0014 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000099 | 0.000097 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative tumor suppressor gene that may be implicated in the origin and progression of lung cancer. {ECO:0000269|PubMed:17260017}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- LoFtool
- 0.228
- RVIS EVS
- 0.64
- RVIS percentile EVS
- 84.05
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0757
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |