THUMPD2

THUMP domain containing 2, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 2:39736060-39779267

Previous symbols: [ "C2orf8" ]

Links

ENSG00000138050 ∙ NCBI:80745 ∙ OMIM:611751 ∙ HGNC:14890 ∙ Uniprot:Q9BTF0 ∙ 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 THUMPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THUMPD2 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			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	0	0

Variants in THUMPD2

This is a list of pathogenic ClinVar variants found in the THUMPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-39736751-T-A		not specified	Uncertain significance (Aug 14, 2023)
2-39736814-A-T		not specified	Uncertain significance (Aug 21, 2024)
2-39736856-T-C		not specified	Uncertain significance (Mar 06, 2023)
2-39736883-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-39736941-G-T		not specified	Uncertain significance (Jun 02, 2023)
2-39736945-A-T		not specified	Uncertain significance (Jul 13, 2021)
2-39736967-T-C		not specified	Uncertain significance (Dec 18, 2023)
2-39737006-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-39744386-G-T		not specified	Uncertain significance (Jan 30, 2024)
2-39744407-C-G		not specified	Uncertain significance (Oct 12, 2024)
2-39744414-A-T		not specified	Uncertain significance (Oct 29, 2024)
2-39744455-C-T		not specified	Uncertain significance (Aug 04, 2023)
2-39744466-G-A		not specified	Uncertain significance (Aug 28, 2024)
2-39755390-G-C		not specified	Uncertain significance (Dec 20, 2023)
2-39755399-T-C		not specified	Uncertain significance (Dec 03, 2021)
2-39755923-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-39755934-C-A		not specified	Uncertain significance (Jan 02, 2024)
2-39755935-A-G		not specified	Uncertain significance (Apr 06, 2024)
2-39755959-G-C		not specified	Uncertain significance (Feb 15, 2023)
2-39761336-T-G		not specified	Uncertain significance (Apr 08, 2022)
2-39761339-C-G		not specified	Uncertain significance (Jan 04, 2022)
2-39761354-T-C		not specified	Uncertain significance (Dec 13, 2022)
2-39761362-G-A		not specified	Uncertain significance (Oct 03, 2023)
2-39761368-G-A		not specified	Uncertain significance (Jul 05, 2023)
2-39761387-T-C		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THUMPD2	protein_coding	protein_coding	ENST00000505747	10	43208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.54e-9	0.376	125666	0	77	125743	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.617	264	237	1.11	0.0000112	3293
Missense in Polyphen		86	79.439	1.0826		1080
Synonymous	-0.399	90	85.3	1.05	0.00000442	926
Loss of Function	0.915	16	20.5	0.782	9.50e-7	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000651	0.000651
Ashkenazi Jewish	0.000110	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00167	0.00166
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000155	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.123
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.372

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thumpd2

Gene ontology

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