IQGAP3
Basic information
Region (hg38): 1:156525405-156572604
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (230 variants)
- IQGAP3-related_disorder (32 variants)
- not_provided (18 variants)
- Motor_and_sensory_neuropathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQGAP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178229.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 17 | 20 | ||||
missense | 222 | 19 | 247 | |||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 225 | 36 | 9 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IQGAP3 | protein_coding | protein_coding | ENST00000361170 | 38 | 47200 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.40e-33 | 0.774 | 125049 | 1 | 698 | 125748 | 0.00278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.642 | 869 | 924 | 0.941 | 0.0000543 | 10560 |
Missense in Polyphen | 287 | 317.21 | 0.90477 | 3688 | ||
Synonymous | 1.71 | 328 | 370 | 0.887 | 0.0000205 | 3261 |
Loss of Function | 2.81 | 67 | 96.8 | 0.692 | 0.00000563 | 988 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00295 | 0.00295 |
Ashkenazi Jewish | 0.00444 | 0.00437 |
East Asian | 0.00158 | 0.00158 |
Finnish | 0.00324 | 0.00324 |
European (Non-Finnish) | 0.00347 | 0.00344 |
Middle Eastern | 0.00158 | 0.00158 |
South Asian | 0.00226 | 0.00226 |
Other | 0.00311 | 0.00310 |
dbNSFP
Source:
- Pathway
- Regulation of actin cytoskeleton - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Signal Transduction;RHO GTPases activate IQGAPs;RHO GTPase Effectors;Signaling by Rho GTPases;RAC1 signaling pathway;CDC42 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- loftool
- 0.641
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 28.02
Haploinsufficiency Scores
- pHI
- 0.230
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.579
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.888
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Iqgap3
- Phenotype
Zebrafish Information Network
- Gene name
- iqgap3
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;activation of MAPK activity;Ras protein signal transduction;regulation of cell size;positive regulation of gene expression;negative regulation of gene expression;positive regulation of mammary gland epithelial cell proliferation;regulation of GTPase activity;ERK1 and ERK2 cascade;cellular response to organic substance
- Cellular component
- cytosol;cell-cell junction;lateral plasma membrane
- Molecular function
- calmodulin binding;Rho GTPase binding;myosin VI light chain binding