ELMO2
Basic information
Region (hg38): 20:46366050-46432985
Links
Phenotypes
GenCC
Source:
- Ramon syndrome (Supportive), mode of inheritance: AR
- primary intraosseous venous malformation (Supportive), mode of inheritance: AR
- primary intraosseous venous malformation (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Vascular malformation, primary intraosseus | AR | Cardiovascular | The condition involves vascular malformation often affecting the vertebral column and the skull, with life-threatening complications after tooth extraction as well as spontaneous severe bleeding episodes, and awareness may allow preventive measures and aggressive management, which may ameliorate morbidity and mortality | Cardiovascular; Musculoskeletal | 11932989; 27476657 |
ClinVar
This is a list of variants' phenotypes submitted to
- Primary intraosseous venous malformation (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMO2 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 | 9 | |||||
missense | 17 | 17 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 3 | ||||
non coding | 17 | 19 | ||||
Total | 2 | 3 | 17 | 9 | 19 |
Variants in ELMO2
This is a list of pathogenic ClinVar variants found in the ELMO2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-46367392-T-C | Inborn genetic diseases | Uncertain significance (Oct 25, 2024) | ||
20-46367442-AG-A | Primary intraosseous venous malformation | Pathogenic (Sep 13, 2016) | ||
20-46367455-G-A | Inborn genetic diseases | Uncertain significance (Nov 01, 2022) | ||
20-46367515-T-C | Inborn genetic diseases | Uncertain significance (Jun 09, 2022) | ||
20-46367543-A-G | Primary intraosseous venous malformation | Benign (Jul 30, 2021) | ||
20-46367615-C-A | Benign (May 12, 2021) | |||
20-46367666-A-G | Benign (May 11, 2021) | |||
20-46368695-GC-G | Benign (May 11, 2021) | |||
20-46368966-C-G | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
20-46369063-C-T | Benign (May 12, 2021) | |||
20-46369117-G-A | Benign (May 11, 2021) | |||
20-46370389-T-C | Benign (May 12, 2021) | |||
20-46370408-C-A | Benign (May 20, 2021) | |||
20-46370526-C-G | Primary intraosseous venous malformation | Likely pathogenic (Jul 16, 2020) | ||
20-46370638-A-G | Benign (May 12, 2021) | |||
20-46371319-A-G | Benign (May 12, 2021) | |||
20-46371382-C-T | Inborn genetic diseases | Uncertain significance (Sep 14, 2022) | ||
20-46371680-T-C | Inborn genetic diseases | Uncertain significance (Jan 29, 2024) | ||
20-46371688-C-G | Inborn genetic diseases | Uncertain significance (Mar 07, 2024) | ||
20-46371783-G-C | Benign (May 12, 2021) | |||
20-46371861-G-A | Primary intraosseous venous malformation | Likely pathogenic (Jun 12, 2024) | ||
20-46371916-G-T | Inborn genetic diseases | Uncertain significance (Dec 22, 2023) | ||
20-46371939-G-A | Primary intraosseous venous malformation | Likely pathogenic (Nov 06, 2021) | ||
20-46371942-T-C | Inborn genetic diseases | Uncertain significance (Feb 14, 2023) | ||
20-46371951-C-G | Inborn genetic diseases | Uncertain significance (Dec 16, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ELMO2 | protein_coding | protein_coding | ENST00000290246 | 20 | 67017 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000104 | 1.00 | 125722 | 0 | 26 | 125748 | 0.000103 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.27 | 235 | 425 | 0.553 | 0.0000243 | 4791 |
Missense in Polyphen | 23 | 101.66 | 0.22624 | 1176 | ||
Synonymous | -0.446 | 162 | 155 | 1.05 | 0.00000845 | 1339 |
Loss of Function | 3.95 | 17 | 45.8 | 0.371 | 0.00000286 | 461 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000235 | 0.000235 |
Ashkenazi Jewish | 0.000198 | 0.000198 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000473 | 0.0000462 |
European (Non-Finnish) | 0.0000969 | 0.0000967 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000672 | 0.0000653 |
Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility. Acts in association with DOCK1 and CRK. Was initially proposed to be required in complex with DOCK1 to activate Rac Rho small GTPases. May enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. {ECO:0000269|PubMed:11595183, ECO:0000269|PubMed:11703939, ECO:0000269|PubMed:20679435, ECO:0000269|PubMed:27476657}.;
- Pathway
- Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Signaling by PTK6;Signal Transduction;VEGFA-VEGFR2 Pathway;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;EGFR1;Regulation of actin dynamics for phagocytic cup formation;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;Signaling by VEGF;Integrin-linked kinase signaling;Signaling by Receptor Tyrosine Kinases
(Consensus)
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- loftool
- 0.725
- rvis_EVS
- -0.82
- rvis_percentile_EVS
- 11.77
Haploinsufficiency Scores
- pHI
- 0.279
- hipred
- Y
- hipred_score
- 0.648
- ghis
- 0.639
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.661
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Elmo2
- Phenotype
Gene ontology
- Biological process
- apoptotic process;cytoskeleton organization;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;cell chemotaxis;cell-cell adhesion
- Cellular component
- cytosol;membrane
- Molecular function
- protein binding;SH3 domain binding;receptor tyrosine kinase binding