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.

• not_specified (83 variants)

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. These statistics are base on transcript: NM_000025264.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			80	3		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	80	3	0

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