CARM1
coactivator associated arginine methyltransferase 1, the group of 7BS protein arginine methyltranferases
Basic information
Region (hg38): 19:10871552-10923075
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (9 variants)
- not provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARM1 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 | 2 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 1 |
Variants in CARM1
This is a list of pathogenic ClinVar variants found in the CARM1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-10871722-C-T | not specified | Uncertain significance (Sep 10, 2021) | ||
| 19-10871746-C-T | not specified | Uncertain significance (Sep 22, 2023) | ||
| 19-10871818-C-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 19-10871866-C-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 19-10871886-G-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 19-10871889-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 19-10871905-G-T | not specified | Uncertain significance (Nov 29, 2023) | ||
| 19-10871920-G-A | not specified | Uncertain significance (Dec 17, 2023) | ||
| 19-10905049-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
| 19-10908054-A-T | Uncertain significance (Nov 13, 2020) | |||
| 19-10908074-C-T | not specified | Uncertain significance (Jul 28, 2021) | ||
| 19-10908093-G-A | not specified | Uncertain significance (Feb 17, 2024) | ||
| 19-10908131-G-T | not specified | Uncertain significance (Feb 02, 2024) | ||
| 19-10912229-G-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 19-10913885-G-A | Benign (May 14, 2018) | |||
| 19-10920520-C-G | not specified | Uncertain significance (Jan 09, 2024) | ||
| 19-10920702-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 19-10921651-C-T | not specified | Uncertain significance (Feb 08, 2023) | ||
| 19-10921652-G-A | Likely benign (Feb 26, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CARM1 | protein_coding | protein_coding | ENST00000327064 | 16 | 51265 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000234 | 125631 | 0 | 1 | 125632 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.25 | 135 | 363 | 0.372 | 0.0000231 | 3976 |
| Missense in Polyphen | 22 | 123.15 | 0.17864 | 1213 | ||
| Synonymous | 0.0691 | 155 | 156 | 0.993 | 0.0000115 | 1213 |
| Loss of Function | 5.08 | 0 | 30.1 | 0.00 | 0.00000137 | 349 |
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) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Methylates (mono- and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in several proteins involved in DNA packaging, transcription regulation, pre-mRNA splicing, and mRNA stability. Recruited to promoters upon gene activation together with histone acetyltransferases from EP300/P300 and p160 families, methylates histone H3 at 'Arg-17' (H3R17me), forming mainly asymmetric dimethylarginine (H3R17me2a), leading to activate transcription via chromatin remodeling. During nuclear hormone receptor activation and TCF7L2/TCF4 activation, acts synergically with EP300/P300 and either one of the p160 histone acetyltransferases NCOA1/SRC1, NCOA2/GRIP1 and NCOA3/ACTR or CTNNB1/beta-catenin to activate transcription. During myogenic transcriptional activation, acts together with NCOA3/ACTR as a coactivator for MEF2C. During monocyte inflammatory stimulation, acts together with EP300/P300 as a coactivator for NF-kappa-B. Acts as coactivator for PPARG, promotes adipocyte differentiation and the accumulation of brown fat tissue. Plays a role in the regulation of pre-mRNA alternative splicing by methylation of splicing factors. Also seems to be involved in p53/TP53 transcriptional activation. Methylates EP300/P300, both at 'Arg- 2142', which may loosen its interaction with NCOA2/GRIP1, and at 'Arg-580' and 'Arg-604' in the KIX domain, which impairs its interaction with CREB and inhibits CREB-dependent transcriptional activation. Also methylates arginine residues in RNA-binding proteins PABPC1, ELAVL1 and ELAV4, which may affect their mRNA- stabilizing properties and the half-life of their target mRNAs. {ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:19405910}.;
- Pathway
- Androgen receptor signaling pathway;Signal Transduction;Gene expression (Transcription);transcription regulation by methyltransferase of carm1;carm1 and regulation of the estrogen receptor;role of erbb2 in signal transduction and oncology;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;Metabolism;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Coregulation of Androgen receptor activity;Signaling by Nuclear Receptors;Chromatin organization;Transcriptional Regulation by TP53;Direct p53 effectors;Estrogen-dependent gene expression;ESR-mediated signaling;Regulation of Androgen receptor activity
(Consensus)
Recessive Scores
- pRec
- 0.283
Intolerance Scores
- loftool
- rvis_EVS
- -1
- rvis_percentile_EVS
- 8.32
Haploinsufficiency Scores
- pHI
- 0.180
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Carm1
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland 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); hematopoietic system phenotype; respiratory system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- carm1
- Affected structure
- slow muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- regulation of growth plate cartilage chondrocyte proliferation;regulation of transcription, DNA-templated;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;aging;positive regulation of cell population proliferation;viral process;histone methylation;regulation of lipid metabolic process;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;intracellular estrogen receptor signaling pathway;negative regulation of protein binding;regulation of intracellular estrogen receptor signaling pathway;histone arginine methylation;histone H3-R2 methylation;histone H3-R17 methylation;positive regulation of fat cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of NF-kappaB transcription factor activity;response to cAMP;endochondral bone morphogenesis;protein localization to chromatin;regulation of mRNA binding;negative regulation of dendrite development
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;RNA polymerase II transcription factor complex
- Molecular function
- transcription coactivator activity;protein binding;beta-catenin binding;protein methyltransferase activity;histone-arginine N-methyltransferase activity;protein-arginine N-methyltransferase activity;nuclear receptor transcription coactivator activity;protein-arginine omega-N asymmetric methyltransferase activity;histone methyltransferase activity (H3-R17 specific);histone methyltransferase activity;protein homodimerization activity;transcription regulatory region DNA binding;lysine-acetylated histone binding