GIMAP2
Basic information
Region (hg38): 7:150685697-150693641
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 GIMAP2 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 | 24 | 28 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 24 | 4 | 0 |
Variants in GIMAP2
This is a list of pathogenic ClinVar variants found in the GIMAP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-150687083-C-G | not specified | Uncertain significance (Feb 02, 2025) | ||
7-150692365-C-G | not specified | Uncertain significance (Feb 26, 2024) | ||
7-150692408-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
7-150692433-A-C | not specified | Uncertain significance (Jan 26, 2023) | ||
7-150692486-G-T | Likely benign (Nov 01, 2022) | |||
7-150692544-C-A | not specified | Uncertain significance (Apr 12, 2022) | ||
7-150692548-T-A | not specified | Likely benign (Jul 06, 2022) | ||
7-150692576-G-A | not specified | Uncertain significance (Nov 14, 2024) | ||
7-150692603-C-T | not specified | Uncertain significance (Aug 30, 2021) | ||
7-150692660-C-G | not specified | Uncertain significance (Sep 14, 2022) | ||
7-150692675-A-C | not specified | Uncertain significance (Oct 08, 2024) | ||
7-150692737-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
7-150692764-A-T | not specified | Uncertain significance (Mar 05, 2024) | ||
7-150692770-G-A | not specified | Likely benign (Apr 12, 2024) | ||
7-150692785-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
7-150692795-A-G | not specified | Uncertain significance (Oct 25, 2023) | ||
7-150692819-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
7-150692855-A-G | not specified | Uncertain significance (Apr 24, 2023) | ||
7-150692860-G-A | not specified | Uncertain significance (Oct 18, 2021) | ||
7-150692900-T-C | not specified | Uncertain significance (Dec 23, 2024) | ||
7-150692985-T-A | not specified | Likely benign (Feb 08, 2025) | ||
7-150693018-A-G | not specified | Uncertain significance (Sep 13, 2022) | ||
7-150693037-A-G | not specified | Uncertain significance (Oct 21, 2021) | ||
7-150693041-G-C | not specified | Uncertain significance (Dec 14, 2023) | ||
7-150693041-G-T | not specified | Uncertain significance (Oct 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GIMAP2 | protein_coding | protein_coding | ENST00000223293 | 2 | 7945 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.405 | 0.479 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.118 | 170 | 174 | 0.975 | 0.00000820 | 2234 |
Missense in Polyphen | 48 | 45.84 | 1.0471 | 596 | ||
Synonymous | 0.486 | 60 | 65.0 | 0.923 | 0.00000298 | 626 |
Loss of Function | 0.974 | 0 | 1.11 | 0.00 | 4.70e-8 | 12 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The heterodimer formed by GIMAP2 and GIMAP7 has GTPase activity. In contrast, GIMAP2 has no GTPase activity by itself. {ECO:0000269|PubMed:23454188}.;
- Pathway
- TYROBP Causal Network
(Consensus)
Recessive Scores
- pRec
- 0.0670
Intolerance Scores
- loftool
- 0.839
- rvis_EVS
- 0.97
- rvis_percentile_EVS
- 90.34
Haploinsufficiency Scores
- pHI
- 0.0576
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.412
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.142
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- Cellular component
- endoplasmic reticulum;lipid droplet;integral component of membrane
- Molecular function
- protein binding;GTP binding;identical protein binding