ICMT

isoprenylcysteine carboxyl methyltransferase, the group of Methyltransferase families

Basic information

Region (hg38): 1:6221192-6235972

Links

ENSG00000116237 ∙ NCBI:23463 ∙ OMIM:605851 ∙ HGNC:5350 ∙ Uniprot:O60725 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ICMT gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

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	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
1-6235806-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: gnomAD

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: dbNSFP

• 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