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.

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.

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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in TDRD3

This is a list of pathogenic ClinVar variants found in the TDRD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-60439714-C-G		not specified	Uncertain significance (Nov 29, 2023)
13-60439728-C-T		not specified	Uncertain significance (Dec 15, 2023)
13-60439740-A-G		not specified	Uncertain significance (Mar 15, 2024)
13-60439752-A-G		not specified	Uncertain significance (Dec 19, 2022)
13-60444711-T-C		not specified	Uncertain significance (Oct 25, 2023)
13-60460437-G-A		not specified	Uncertain significance (Apr 08, 2024)
13-60460446-G-C		not specified	Uncertain significance (Dec 15, 2023)
13-60460500-A-C		not specified	Uncertain significance (Jan 24, 2024)
13-60467269-C-T		not specified	Uncertain significance (Dec 03, 2021)
13-60467284-G-A		not specified	Uncertain significance (Apr 23, 2024)
13-60467350-C-A		not specified	Uncertain significance (Dec 20, 2023)
13-60483836-C-G		not specified	Uncertain significance (Oct 05, 2023)
13-60494518-A-T		not specified	Uncertain significance (Jun 11, 2024)
13-60509840-T-A		not specified	Uncertain significance (Aug 21, 2023)
13-60509902-T-C		not specified	Likely benign (Aug 02, 2023)
13-60510647-G-A		not specified	Uncertain significance (Sep 20, 2023)
13-60510669-A-G		not specified	Uncertain significance (Dec 20, 2023)
13-60510687-C-A		not specified	Uncertain significance (Sep 22, 2023)
13-60528469-G-A		not specified	Uncertain significance (Jan 03, 2022)
13-60528483-C-A		not specified	Uncertain significance (May 03, 2024)
13-60528501-C-G		not specified	Uncertain significance (Sep 22, 2022)
13-60528555-G-A		not specified	Uncertain significance (Apr 22, 2022)
13-60528574-G-A		not specified	Uncertain significance (Oct 06, 2023)
13-60528699-A-C		not specified	Uncertain significance (Dec 28, 2022)
13-60528753-G-C		not specified	Uncertain significance (Sep 07, 2022)

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