TDRD1

tudor domain containing 1, the group of Tudor domain containing|Zinc fingers MYND-type

Basic information

Region (hg38): 10:114179270-114232666

Links

ENSG00000095627 ∙ NCBI:56165 ∙ OMIM:605796 ∙ HGNC:11712 ∙ Uniprot:Q9BXT4 ∙ 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 TDRD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD1 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				2		2
missense		1	56	2	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	56	4	1

Variants in TDRD1

This is a list of pathogenic ClinVar variants found in the TDRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-114187895-A-G		not specified	Uncertain significance (Sep 08, 2024)
10-114187897-G-A		not specified	Uncertain significance (Apr 17, 2023)
10-114187922-A-T		not specified	Uncertain significance (Oct 16, 2024)
10-114187965-G-A		not specified	Uncertain significance (Oct 04, 2024)
10-114187973-C-G		not specified	Uncertain significance (Jun 17, 2024)
10-114187990-C-G		not specified	Uncertain significance (Dec 12, 2022)
10-114188088-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-114188097-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-114190987-G-A		not specified	Uncertain significance (Aug 11, 2021)
10-114190997-C-T		not specified	Uncertain significance (Dec 13, 2023)
10-114191006-A-G		not specified	Uncertain significance (Apr 27, 2022)
10-114199191-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-114199216-A-G		not specified	Uncertain significance (Dec 11, 2023)
10-114199252-C-T		not specified	Uncertain significance (Jan 27, 2022)
10-114201492-C-T			Likely benign (Nov 01, 2023)
10-114201493-G-A		not specified	Uncertain significance (Jul 26, 2021)
10-114201499-A-G		not specified	Uncertain significance (Jan 03, 2022)
10-114202273-C-T		not specified	Uncertain significance (Jan 23, 2024)
10-114203388-G-T		not specified	Uncertain significance (Dec 17, 2023)
10-114203392-C-T		not specified	Uncertain significance (Aug 18, 2021)
10-114203462-G-A		not specified	Uncertain significance (Aug 28, 2024)
10-114203473-C-A		Male infertility	Likely pathogenic (Feb 27, 2023)
10-114203493-T-A		not specified	Uncertain significance (Sep 27, 2022)
10-114203559-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-114204088-A-G		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD1	protein_coding	protein_coding	ENST00000251864	25	53035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000117	125733	0	9	125742	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	509	606	0.840	0.0000293	7821
Missense in Polyphen		196	273.03	0.71786		3655
Synonymous	-1.59	247	217	1.14	0.0000114	2158
Loss of Function	6.59	5	60.1	0.0832	0.00000280	820

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for the germline integrity. 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 governs the methylation and subsequent repression of transposons. Required for the localization of Piwi proteins to the meiotic nuage. Involved in the piRNA metabolic process by ensuring the entry of correct transcripts into the normal piRNA pool and limiting the entry of cellular transcripts into the piRNA pathway. May act by allowing the recruitment of piRNA biogenesis or loading factors that ensure the correct entry of transcripts and piRNAs into Piwi proteins (By similarity). {ECO:0000250}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.94

Haploinsufficiency Scores

• pHI: 0.0713
• hipred: N
• hipred_score: 0.273
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrd1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: tdrd1
• Affected structure: primordial germ cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: multicellular organism development;germ cell development;spermatogenesis;gene silencing by RNA;piRNA metabolic process;DNA methylation involved in gamete generation;meiotic cell cycle
• Cellular component: cytoplasm;chromatoid body;P granule;pi-body
• Molecular function: metal ion binding