ICMT
isoprenylcysteine carboxyl methyltransferase, the group of Methyltransferase families
Basic information
Region (hg38): 1:6221193-6235972
Links
Phenotypes
GenCC
Source:
No genCC data.
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 ICMT 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 | 1 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in ICMT
This is a list of pathogenic ClinVar variants found in the ICMT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-6225106-T-C | not specified | Uncertain significance (Mar 31, 2023) | ||
| 1-6225210-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 1-6232010-C-T | Benign (Dec 31, 2019) | |||
| 1-6232047-G-A | not specified | Uncertain significance (May 09, 2023) | ||
| 1-6233485-A-G | not specified | Uncertain significance (Sep 29, 2022) | ||
| 1-6235794-C-T | not specified | Uncertain significance (Oct 07, 2024) | ||
| 1-6235806-C-T | not specified | Uncertain significance (Mar 07, 2024) | ||
| 1-6235857-C-A | not specified | Uncertain significance (Jul 30, 2023) | ||
| 1-6235886-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-6235907-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-6235908-C-A | not specified | Uncertain significance (Jul 19, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ICMT | protein_coding | protein_coding | ENST00000343813 | 5 | 14780 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.794 | 0.206 | 125740 | 0 | 7 | 125747 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.42 | 54 | 132 | 0.409 | 0.00000718 | 1790 |
| Missense in Polyphen | 9 | 33.962 | 0.265 | 396 | ||
| Synonymous | 0.657 | 50 | 56.3 | 0.889 | 0.00000338 | 598 |
| Loss of Function | 2.97 | 2 | 14.0 | 0.143 | 8.01e-7 | 144 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the post-translational methylation of isoprenylated C-terminal cysteine residues.;
- Pathway
- Terpenoid backbone biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.0833
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.662
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.417
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.916
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Icmt
- Phenotype
- liver/biliary system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- cellular protein modification process;C-terminal protein methylation;protein targeting to membrane;post-translational protein modification
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane
- Molecular function
- protein C-terminal carboxyl O-methyltransferase activity;protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity