DIMT1

DIM1 rRNA methyltransferase and ribosome maturation factor, the group of 7BS N6-adenosine DNA/RNA methyltransferases|Ribosomal biogenesis factors

Basic information

Region (hg38): 5:62347283-62403943

Previous symbols: [ "DIMT1L" ]

Links

ENSG00000086189 ∙ NCBI:27292 ∙ OMIM:612499 ∙ HGNC:30217 ∙ Uniprot:Q9UNQ2 ∙ 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 DIMT1 gene.

• not provided (373 variants)
• Inborn genetic diseases (16 variants)
• not specified (14 variants)
• Complex cortical dysplasia with other brain malformations 3 (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIMT1 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding	1	3	120	177	81	382
Total	1	3	129	177	81

Variants in DIMT1

This is a list of pathogenic ClinVar variants found in the DIMT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-62347815-G-A			Likely benign (Nov 27, 2018)
5-62347834-G-A			Benign (Jun 14, 2018)
5-62347942-G-A			Benign (Jul 11, 2018)
5-62347989-G-A			Benign (Jun 14, 2018)
5-62348031-G-T			Likely benign (Nov 28, 2022)
5-62348033-A-T			Benign (Jan 08, 2024)
5-62348035-G-T			Likely benign (Nov 28, 2022)
5-62348037-G-C			Likely benign (Dec 13, 2023)
5-62348041-T-C			Likely benign (Jul 20, 2023)
5-62348078-C-T			Benign (Jul 27, 2023)
5-62348083-C-A		not specified • KIF2A-related disorder	Benign (Jan 24, 2024)
5-62348084-C-T			Likely benign (Oct 13, 2023)
5-62348094-A-G			Uncertain significance (Feb 14, 2023)
5-62348104-T-A			Likely benign (Jun 15, 2022)
5-62348105-G-A		Complex cortical dysplasia with other brain malformations 3	Likely pathogenic (Nov 10, 2023)
5-62348112-G-A		Complex cortical dysplasia with other brain malformations 3	Uncertain significance (-)
5-62348114-C-A		not specified • KIF2A-related disorder	Likely benign (Jan 24, 2024)
5-62348126-C-T			Uncertain significance (Aug 23, 2021)
5-62348135-G-A			Uncertain significance (Aug 07, 2022)
5-62348135-G-T			Benign (Aug 17, 2023)
5-62348147-A-C			Uncertain significance (Sep 11, 2023)
5-62348151-T-C			Uncertain significance (Jul 29, 2021)
5-62348161-T-A			Likely benign (Oct 22, 2023)
5-62348173-TG-T			Likely benign (May 26, 2022)
5-62348175-A-T			Likely benign (May 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DIMT1	protein_coding	protein_coding	ENST00000199320	12	16686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.91e-7	0.821	125660	0	87	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	160	172	0.931	0.00000841	2047
Missense in Polyphen		61	63.504	0.96058		801
Synonymous	0.0192	58	58.2	0.997	0.00000269	595
Loss of Function	1.44	13	19.9	0.652	0.00000109	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000418	0.000413
Middle Eastern	0.000544	0.000544
South Asian	0.000296	0.000294
Other	0.000359	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA in the 40S particle (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604). {ECO:0000269|PubMed:25851604}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.376

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.677
• ghis: 0.671

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dimt1

Gene ontology

• Biological process: rRNA methylation;positive regulation of rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;mitochondrial matrix;cytosol
• Molecular function: rRNA (adenine-N6,N6-)-dimethyltransferase activity;RNA binding;18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity