TDRD5

tudor domain containing 5, the group of Tudor domain containing

Basic information

Region (hg38): 1:179591613-179691272

Links

ENSG00000162782 ∙ NCBI:163589 ∙ OMIM:617748 ∙ HGNC:20614 ∙ Uniprot:Q8NAT2 ∙ 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 TDRD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD5 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				1	2	3
missense			38	8	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	9	3

Variants in TDRD5

This is a list of pathogenic ClinVar variants found in the TDRD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-179592662-G-A		not specified	Uncertain significance (May 16, 2022)
1-179592766-C-T		not specified	Uncertain significance (Aug 28, 2023)
1-179592781-C-G		not specified	Uncertain significance (Apr 25, 2022)
1-179592795-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-179592797-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-179592833-C-A		not specified	Uncertain significance (Dec 02, 2021)
1-179593537-A-G		not specified	Uncertain significance (Feb 17, 2023)
1-179593571-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-179593726-T-A		not specified	Uncertain significance (Nov 23, 2021)
1-179593754-T-C			Uncertain significance (-)
1-179593801-A-G		not specified	Uncertain significance (Nov 17, 2023)
1-179595682-T-G		not specified	Uncertain significance (Dec 07, 2023)
1-179595685-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-179595698-A-G			Benign (May 30, 2018)
1-179595714-A-G		not specified	Uncertain significance (May 08, 2023)
1-179618606-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-179618607-C-A		not specified	Uncertain significance (Jun 27, 2022)
1-179630814-T-A		not specified	Uncertain significance (Apr 29, 2024)
1-179630877-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-179634508-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-179634520-C-G		not specified	Uncertain significance (Jul 25, 2023)
1-179634569-A-C		not specified	Likely benign (Jan 31, 2024)
1-179634600-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-179635722-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-179635769-G-C		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD5	protein_coding	protein_coding	ENST00000444136	17	99660

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0275	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	416	540	0.770	0.0000280	6736
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000167	0.000163
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0796
• hipred: Y
• hipred_score: 0.535
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrd5
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: spermatid development;P granule organization;DNA methylation involved in gamete generation
• Cellular component: chromatoid body;pi-body