THUMPD3

THUMP domain containing 3, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 3:9362971-9386791

Links

ENSG00000134077 ∙ NCBI:25917 ∙ ∙ HGNC:24493 ∙ Uniprot:Q9BV44 ∙ 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 THUMPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THUMPD3 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			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	0

Variants in THUMPD3

This is a list of pathogenic ClinVar variants found in the THUMPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9365159-G-A		not specified	Likely benign (Apr 25, 2022)
3-9365183-A-G		not specified	Uncertain significance (Oct 13, 2023)
3-9365193-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-9365210-T-C		not specified	Uncertain significance (May 15, 2023)
3-9365247-T-A		not specified	Uncertain significance (Jan 07, 2022)
3-9365279-G-A		not specified	Uncertain significance (Sep 20, 2024)
3-9366911-C-A		not specified	Uncertain significance (Aug 12, 2021)
3-9366942-T-C		not specified	Uncertain significance (Jul 19, 2022)
3-9366947-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-9366953-G-C		not specified	Uncertain significance (Dec 04, 2024)
3-9366974-A-G		not specified	Uncertain significance (Jun 16, 2024)
3-9371165-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-9371264-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-9371274-C-T		not specified	Uncertain significance (Oct 17, 2023)
3-9371314-G-C		not specified	Uncertain significance (Jan 10, 2022)
3-9371316-A-T		not specified	Uncertain significance (Nov 03, 2023)
3-9371319-T-G		not specified	Uncertain significance (Dec 11, 2023)
3-9371339-G-T		not specified	Uncertain significance (Feb 13, 2024)
3-9371348-T-C		not specified	Uncertain significance (Feb 22, 2023)
3-9371378-A-G		not specified	Uncertain significance (Jun 22, 2023)
3-9371393-C-T		not specified	Uncertain significance (Apr 23, 2024)
3-9371396-C-G		not specified	Likely benign (Aug 02, 2023)
3-9371409-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-9371424-A-G		not specified	Uncertain significance (Oct 20, 2024)
3-9371429-G-C		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THUMPD3	protein_coding	protein_coding	ENST00000345094	9	23950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.17e-14	0.0684	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.414	290	271	1.07	0.0000136	3333
Missense in Polyphen		67	70.747	0.94704		872
Synonymous	0.888	82	92.9	0.883	0.00000470	952
Loss of Function	0.582	22	25.2	0.875	0.00000142	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00226	0.00226
Ashkenazi Jewish	0.00	0.00
East Asian	0.000443	0.000435
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000522	0.000519
Middle Eastern	0.000443	0.000435
South Asian	0.000621	0.000621
Other	0.000667	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• loftool: 0.993
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.204
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thumpd3

Gene ontology

• Biological process: tRNA methylation
• Cellular component: nucleolus;cytosol
• Molecular function: RNA binding;tRNA (guanine) methyltransferase activity