TDRD5

protein-coding

tudor domain containing 5, the group of Tudor domain containing

Gene summary

Predicted to be involved in P granule organization; spermatid development; and transposable element silencing by piRNA-mediated DNA methylation. Predicted to be located in chromatoid body and pi-body. Predicted to be active in synapse. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001199085.3

Inheritance

—

ClinVar variants

U:112B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr1:179,591,613-179,691,272

External References & Databases

Ensembl (ENSG00000162782)

Transcript & Mutation Effects

hg38 • Region Span ~99.7 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 TDRD5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001199085.3. 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				1 clinvar	2 clinvar	3
missense			107 clinvar	9 clinvar	1 clinvar	117
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	112	10	3	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199085.3	RefSeq	NP_001186014.1	17	MANE Select
ENST00000444136.6	Ensembl	ENSP00000406052.1	17	MANE Select
NM_001199089.3	RefSeq	NP_001186018.1	17	Standard
NM_001199091.2	RefSeq	NP_001186020.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatid development
P granule organization
DNA methylation involved in gamete generation

Cellular Component

chromatoid body
pi-body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000444136
Coding exons: 17
Length: 99660
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	416	540	0.770	0.0000280	6736
Missense (PolyPhen)		88	166.31	0.52914		2127
Synonymous	-0.702	208	196	1.06	0.0000101	1974
Loss of Function	5.64	10	55.2	0.181	0.00000315	667

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00017	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required during spermiogenesis to participate in the repression transposable elements and prevent their mobilization, which is essential for the germline integrity. Probably acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Required for chromatoid body (CB) assembly (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.578
RVIS EVS: 0.69
RVIS percentile EVS: 85.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.178

Gene Damage Prediction

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