TDRD12

tudor domain containing 12, the group of Tudor domain containing

Basic information

Region (hg38): 19:32719753-32829580

Links

ENSG00000173809 ∙ NCBI:91646 ∙ ∙ HGNC:25044 ∙ Uniprot:Q587J7 ∙ 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 TDRD12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD12 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	25	2	1	29
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	4	25	4	1

Variants in TDRD12

This is a list of pathogenic ClinVar variants found in the TDRD12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32731758-A-G		not specified	Uncertain significance (Jan 26, 2023)
19-32731782-C-G		not specified	Uncertain significance (Aug 04, 2022)
19-32731791-G-A		not specified	Uncertain significance (Jan 22, 2024)
19-32738860-G-T		not specified	Uncertain significance (Sep 29, 2023)
19-32738905-T-C		not specified	Uncertain significance (Sep 13, 2023)
19-32738917-C-A		not specified	Uncertain significance (Jan 03, 2024)
19-32738925-G-A		not specified	Uncertain significance (Aug 04, 2021)
19-32738955-G-A		not specified	Uncertain significance (May 30, 2024)
19-32738959-A-C		Male infertility	Uncertain significance (Feb 27, 2023)
19-32742791-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-32742794-G-T		not specified	Uncertain significance (Sep 29, 2022)
19-32742843-A-G		not specified	Uncertain significance (May 04, 2022)
19-32742881-C-G		not specified	Uncertain significance (Jun 07, 2024)
19-32748496-A-G		not specified	Likely benign (Mar 02, 2023)
19-32748501-G-T		not specified	Uncertain significance (Nov 22, 2023)
19-32748510-T-C		not specified	Uncertain significance (Apr 06, 2022)
19-32748513-T-C		not specified	Uncertain significance (Nov 30, 2022)
19-32755992-G-A		not specified	Uncertain significance (Jun 22, 2024)
19-32756002-A-G		Male infertility • not specified	Uncertain significance (Feb 27, 2023)
19-32756043-C-T		not specified	Uncertain significance (May 25, 2022)
19-32756053-A-C		not specified	Uncertain significance (Apr 28, 2022)
19-32756161-A-G		not specified	Uncertain significance (Jun 12, 2023)
19-32757038-A-G		not specified	Uncertain significance (Nov 07, 2022)
19-32757068-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-32757118-G-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD12	protein_coding	protein_coding	ENST00000421545	13	109825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.92e-13	0.0395	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.694	142	167	0.849	0.00000799	2597
Missense in Polyphen		41	41.47	0.98866		678
Synonymous	2.24	39	61.3	0.636	0.00000332	678
Loss of Function	0.242	20	21.2	0.943	0.00000105	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ATP-binding RNA helicase required during spermatogenesis to repress 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. Involved in the secondary piRNAs metabolic process. Acts via the PET complex, a multiprotein complex required during the secondary piRNAs metabolic process for the PIWIL2 slicing-triggered loading of PIWIL4 piRNAs. {ECO:0000250|UniProtKB:Q9CWU0}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Intolerance Scores

• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.91

Haploinsufficiency Scores

• pHI: 0.207

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0625

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrd12
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: tdrd12
• Affected structure: spermatogonium
• Phenotype tag: abnormal
• Phenotype quality: deformed

Gene ontology

• Biological process: male meiotic nuclear division;multicellular organism development;spermatogenesis;fertilization;cell differentiation;gene silencing by RNA;piRNA metabolic process;DNA methylation involved in gamete generation
• Cellular component: cellular_component;PET complex
• Molecular function: molecular_function;nucleic acid binding;helicase activity;ATP binding