MNAT1
MNAT1 component of CDK activating kinase, the group of Nucleotide excision repair|CDK activating kinase complex|Ring finger proteins
Basic information
Region (hg38): 14:60734742-60969965
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 MNAT1 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 | 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 | 9 | 1 | 1 |
Variants in MNAT1
This is a list of pathogenic ClinVar variants found in the MNAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-60734929-G-A | not specified | Uncertain significance (Mar 15, 2024) | ||
| 14-60796291-A-G | not specified | Uncertain significance (Jan 17, 2023) | ||
| 14-60796296-A-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 14-60796349-C-T | Benign (Dec 31, 2019) | |||
| 14-60808335-G-C | Likely benign (Aug 24, 2018) | |||
| 14-60808339-A-C | not specified | Uncertain significance (May 13, 2024) | ||
| 14-60808348-G-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 14-60808370-A-G | not specified | Uncertain significance (Feb 14, 2024) | ||
| 14-60808394-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 14-60811997-A-G | not specified | Uncertain significance (Sep 27, 2022) | ||
| 14-60812030-G-A | not specified | Uncertain significance (Oct 20, 2023) | ||
| 14-60812062-C-G | not specified | Uncertain significance (Jun 02, 2023) | ||
| 14-60812087-T-C | not specified | Uncertain significance (Jun 04, 2024) | ||
| 14-60818810-C-T | not specified | Uncertain significance (Sep 07, 2022) | ||
| 14-60879736-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 14-60879819-A-G | not specified | Uncertain significance (May 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MNAT1 | protein_coding | protein_coding | ENST00000261245 | 8 | 235212 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.31e-12 | 0.0260 | 125708 | 0 | 40 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.718 | 123 | 148 | 0.834 | 0.00000650 | 2026 |
| Missense in Polyphen | 46 | 52.692 | 0.87301 | 772 | ||
| Synonymous | 0.473 | 48 | 52.4 | 0.917 | 0.00000237 | 538 |
| Loss of Function | -0.105 | 18 | 17.5 | 1.03 | 8.92e-7 | 230 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000348 | 0.000339 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000186 | 0.000185 |
| European (Non-Finnish) | 0.000153 | 0.000149 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000370 | 0.000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II. {ECO:0000269|PubMed:10024882}.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Eukaryotic Transcription Initiation;G1 to S cell cycle control;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Formation of the HIV-1 Early Elongation Complex;Epigenetic regulation of gene expression;Gene expression (Transcription);sonic hedgehog receptor ptc1 regulates cell cycle;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;Formation of HIV elongation complex in the absence of HIV Tat;Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Formation of RNA Pol II elongation complex ;RNA Polymerase I Promoter Clearance;HIV Transcription Initiation;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;Cyclin D associated events in G1;G1 Phase;RNA Polymerase II Transcription Elongation;Cyclin E associated events during G1/S transition ;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;RNA Polymerase II Promoter Escape;RNA Polymerase I Chain Elongation;AndrogenReceptor;S Phase;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;Cyclin A/B1/B2 associated events during G2/M transition;IL-7 signaling;TP53 Regulates Transcription of DNA Repair Genes;G2/M Transition;Mitotic G2-G2/M phases;JAK STAT pathway and regulation;G1/S Transition;EPO signaling;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Cell Cycle;Formation of Incision Complex in GG-NER;VEGF;Global Genome Nucleotide Excision Repair (GG-NER);Cell Cycle, Mitotic;Formation of TC-NER Pre-Incision Complex;Transcriptional regulation by RUNX1;Retinoic acid receptors-mediated signaling;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.281
Intolerance Scores
- loftool
- 0.866
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.909
- hipred
- Y
- hipred_score
- 0.721
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mnat1
- Phenotype
- growth/size/body region phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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; reproductive 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);
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;DNA repair;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, preincision complex assembly;regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;protein phosphorylation;adult heart development;cell population proliferation;ventricular system development;negative regulation of apoptotic process;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of transcription by RNA polymerase II;positive regulation of smooth muscle cell proliferation;response to calcium ion;protein-containing complex assembly;negative regulation of DNA helicase activity
- Cellular component
- nucleoplasm;transcription factor TFIIH holo complex;cytosol;cyclin-dependent protein kinase activating kinase holoenzyme complex
- Molecular function
- protein binding;DNA-dependent ATPase activity;zinc ion binding;RNA polymerase II CTD heptapeptide repeat kinase activity;protein N-terminus binding;cyclin-dependent protein serine/threonine kinase activator activity