TDRD3

tudor domain containing 3, the group of Tudor domain containing

Basic information

Region (hg38): 13:60396457-60573878

Links

ENSG00000083544

∙ NCBI:81550 ∙ OMIM:614392 ∙ HGNC:20612 ∙ Uniprot:Q9H7E2 ∙ 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 TDRD3 gene.

not_specified (80 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001146070.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			79 clinvar	1 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD3	protein_coding	protein_coding	ENST00000535286	13	177422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000410	1.00	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	306	385	0.795	0.0000193	4869
Missense in Polyphen		102	146.17	0.6978		1741
Synonymous	0.751	122	133	0.917	0.00000665	1419
Loss of Function	3.41	16	38.9	0.411	0.00000232	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000653	0.000642
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000488	0.0000462
European (Non-Finnish)	0.000324	0.000316
Middle Eastern	0.000111	0.000109
South Asian	0.0000333	0.0000327
Other	0.000683	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine- methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. {ECO:0000269|PubMed:15955813, ECO:0000269|PubMed:18632687, ECO:0000269|PubMed:21172665}.;

Recessive Scores

pRec: 0.0992

Intolerance Scores

loftool: 0.0560
rvis_EVS: -0.42
rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

pHI: 0.0755
hipred: N
hipred_score: 0.463
ghis: 0.578

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tdrd3
Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype;

Gene ontology

Biological process: chromatin organization;positive regulation of nucleic acid-templated transcription
Cellular component: nucleus;nucleoplasm;Golgi apparatus;cytosol;exon-exon junction complex
Molecular function: chromatin binding;transcription coactivator activity;RNA binding;protein binding;methylated histone binding