ESM1
Basic information
Region (hg38): 5:54977866-55022671
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESM1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 1 | 0 |
Variants in ESM1
This is a list of pathogenic ClinVar variants found in the ESM1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-54979337-G-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 5-54979370-C-T | not specified | Likely benign (Aug 08, 2022) | ||
| 5-54979415-C-A | not specified | Uncertain significance (May 23, 2023) | ||
| 5-54979415-C-T | not specified | Uncertain significance (Feb 03, 2022) | ||
| 5-54981998-C-T | Benign (Jun 19, 2018) | |||
| 5-54985468-A-T | not specified | Uncertain significance (Apr 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ESM1 | protein_coding | protein_coding | ENST00000381405 | 3 | 44808 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.212 | 0.752 | 125730 | 0 | 6 | 125736 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.981 | 85 | 115 | 0.742 | 0.00000659 | 1208 |
| Missense in Polyphen | 25 | 46.137 | 0.54186 | 463 | ||
| Synonymous | 0.485 | 42 | 46.2 | 0.909 | 0.00000294 | 353 |
| Loss of Function | 1.75 | 2 | 6.99 | 0.286 | 3.46e-7 | 84 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in angiogenesis; promotes angiogenic sprouting. May have potent implications in lung endothelial cell-leukocyte interactions. {ECO:0000269|PubMed:20616313}.;
- Pathway
- Gastric Cancer Network 1
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.325
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.131
- hipred
- N
- hipred_score
- 0.385
- ghis
- 0.399
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Esm1
- Phenotype
Gene ontology
- Biological process
- angiogenesis;regulation of cell growth;sprouting angiogenesis;positive regulation of cell population proliferation;positive regulation of hepatocyte growth factor receptor signaling pathway
- Cellular component
- extracellular region
- Molecular function
- hepatocyte growth factor receptor binding;integrin binding;insulin-like growth factor binding