GMFG
Basic information
Region (hg38): 19:39328353-39342372
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 GMFG 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 | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in GMFG
This is a list of pathogenic ClinVar variants found in the GMFG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-39328481-C-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 19-39328518-T-A | not specified | Uncertain significance (Oct 16, 2024) | ||
| 19-39329600-A-C | not specified | Uncertain significance (Mar 14, 2023) | ||
| 19-39333092-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 19-39333092-G-C | not specified | Uncertain significance (Jul 14, 2023) | ||
| 19-39335266-A-G | not specified | Uncertain significance (Jun 22, 2023) | ||
| 19-39335277-A-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 19-39335286-A-G | not specified | Uncertain significance (Dec 30, 2024) | ||
| 19-39335292-C-T | not specified | Uncertain significance (Dec 16, 2024) | ||
| 19-39335293-G-C | not specified | Uncertain significance (Mar 12, 2024) | ||
| 19-39335453-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 19-39335459-C-G | not specified | Uncertain significance (Dec 22, 2023) | ||
| 19-39335471-G-A | not specified | Uncertain significance (Jul 18, 2024) | ||
| 19-39335500-G-A | not specified | Uncertain significance (Apr 17, 2023) | ||
| 19-39335507-C-T | not specified | Uncertain significance (Nov 10, 2024) | ||
| 19-39335509-T-G | not specified | Uncertain significance (Jun 02, 2023) | ||
| 19-39335510-C-T | not specified | Uncertain significance (Oct 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GMFG | protein_coding | protein_coding | ENST00000597595 | 7 | 14020 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.18e-8 | 0.105 | 125674 | 0 | 74 | 125748 | 0.000294 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.180 | 79 | 83.6 | 0.945 | 0.00000469 | 942 |
| Missense in Polyphen | 25 | 29.308 | 0.85301 | 307 | ||
| Synonymous | -0.460 | 33 | 29.8 | 1.11 | 0.00000174 | 243 |
| Loss of Function | -0.0876 | 12 | 11.7 | 1.03 | 6.68e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000699 | 0.000697 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000196 | 0.000193 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00105 | 0.00105 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.781
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.544
- hipred
- N
- hipred_score
- 0.279
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.315
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gmfg
- Phenotype
Zebrafish Information Network
- Gene name
- gmfg
- Affected structure
- dorsal longitudinal anastomotic vessel
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic
Gene ontology
- Biological process
- protein phosphorylation;negative regulation of protein kinase activity;regulation of signaling receptor activity;negative regulation of Arp2/3 complex-mediated actin nucleation;positive regulation of catalytic activity;neutrophil degranulation;actin filament debranching;regulation of actin cytoskeleton reorganization
- Cellular component
- extracellular region;actin cortical patch;secretory granule lumen;ficolin-1-rich granule lumen
- Molecular function
- actin binding;protein kinase inhibitor activity;enzyme activator activity;growth factor activity;Arp2/3 complex binding