EGFLAM
protein-codingEGF like, fibronectin type III and laminin G domains, the group of Fibronectin type III domain containing
Gene summary
Predicted to enable calcium ion binding activity; glycosaminoglycan binding activity; and molecular adaptor activity. Predicted to be involved in signal transduction and synapse assembly. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Part of cell surface. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~207.1 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 EGFLAM variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152403.4. 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 | 6 | 3 | 1 | 10 | ||
| missense | 175 | 5 | 180 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 183 | 8 | 1 | 192 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689616.2 | 22 | MANE Select | |
| Ensembl | ENSP00000313084.5 | 22 | MANE Select | |
| RefSeq | NP_001192230.1 | 23 | Standard | |
| RefSeq | NP_877950.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of cell-substrate adhesion
- peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan
- extracellular matrix organization
Molecular Function
- calcium ion binding
- glycosaminoglycan binding
Cellular Component
- basement membrane
- interstitial matrix
- cell junction
- synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000354891
- Coding exons
- 23
- Length
- 206613
- Individuals with no LoFs
- 125581
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 167
- Defined
- 125748
- p
- 0.000664
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.334 | 571 | 594 | 0.961 | 0.0000330 | 6635 |
| Missense (PolyPhen) | 196 | 224.7 | 0.87228 | 2615 | ||
| Synonymous | -1.01 | 255 | 235 | 1.08 | 0.0000141 | 2008 |
| Loss of Function | 1.98 | 37 | 52.5 | 0.705 | 0.00000273 | 598 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.00058 | 0.00058 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.0012 | 0.0012 | notable |
| Finnish | 0.00095 | 0.00083 | rare |
| European (Non-Finnish) | 0.00033 | 0.00033 | rare |
| South Asian | 0.0018 | 0.0018 | notable |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in both the retinal photoreceptor ribbon synapse formation and physiological functions of visual perception. Necessary for proper bipolar dendritic tip apposition to the photoreceptor ribbon synapse. Promotes matrix assembly and cell adhesiveness (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.738
Intolerance Scores
- LoFtool
- 0.520
- RVIS EVS
- 1.06
- RVIS percentile EVS
- 91.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.328
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |