TDRD3

protein-coding

tudor domain containing 3, the group of Tudor domain containing

Gene summary

Enables chromatin binding activity; histone reader activity; and transcription coactivator activity. Predicted to be involved in siRNA-mediated heterochromatin formation. Located in cytosol; exon-exon junction complex; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001146070.2

Inheritance

—

ClinVar variants

U:93B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr13:60,396,457-60,573,878

External References & Databases

Ensembl (ENSG00000083544)

Transcript & Mutation Effects

hg38 • Region Span ~177.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TDRD3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 89

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001146070.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			90 clinvar	1 clinvar		91
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	93	1	0	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001146070.2	RefSeq	NP_001139542.1	13	MANE Select
ENST00000377881.8	Ensembl	ENSP00000367113.2	13	MANE Select
NM_001146071.1	RefSeq	NP_001139543.1	10	Standard
NM_030794.2	RefSeq	NP_110421.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromatin organization
positive regulation of nucleic acid-templated transcription

Molecular Function

chromatin binding
transcription coactivator activity
RNA binding
protein binding
methylated histone binding

Cellular Component

nucleus
nucleoplasm
Golgi apparatus
cytosol
exon-exon junction complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000535286
Coding exons: 13
Length: 177422
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.43	306	385	0.795	0.0000193	4869
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.000033	0.000033	rare
Other	0.00068	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.961

Gene Damage Prediction

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