MNAT1

MNAT1 component of CDK activating kinase, the group of Nucleotide excision repair|CDK activating kinase complex|Ring finger proteins

Basic information

Region (hg38): 14:60734741-60969965

Links

ENSG00000020426 ∙ NCBI:4331 ∙ OMIM:602659 ∙ HGNC:7181 ∙ Uniprot:P51948 ∙ 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 MNAT1 gene.

• Inborn genetic diseases (5 variants)
• not provided (2 variants)

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	1
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	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
14-60796291-A-G		not specified	Uncertain significance (Jan 17, 2023)
14-60796349-C-T			Benign (Dec 31, 2019)
14-60808335-G-C			Likely benign (Aug 24, 2018)
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)
14-60818810-C-T		not specified	Uncertain significance (Sep 07, 2022)
14-60879736-C-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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