TDRKH

tudor and KH domain containing, the group of Tudor domain containing

Basic information

Region (hg38): 1:151770106-151791416

Links

ENSG00000182134 ∙ NCBI:11022 ∙ OMIM:609501 ∙ HGNC:11713 ∙ Uniprot:Q9Y2W6 ∙ 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 TDRKH gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRKH 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						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in TDRKH

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

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

Position	Type	Phenotype	Significance	ClinVar
1-151774486-C-G		not specified	Uncertain significance (Sep 20, 2023)
1-151774749-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-151774806-C-A		not specified	Uncertain significance (Aug 11, 2022)
1-151775087-A-T		not specified	Uncertain significance (Oct 06, 2021)
1-151775424-T-C		not specified	Uncertain significance (Mar 31, 2022)
1-151775453-T-C		not specified	Uncertain significance (Jan 25, 2023)
1-151775533-C-G		not specified	Uncertain significance (Dec 13, 2021)
1-151775834-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-151776183-C-T		not specified	Uncertain significance (May 16, 2022)
1-151776198-C-T		not specified	Uncertain significance (Nov 03, 2022)
1-151776480-T-A		Azoospermia	Pathogenic (Dec 20, 2021)
1-151776497-C-T		Distal spinal muscular atrophy	Conflicting classifications of pathogenicity (Oct 18, 2023)
1-151778790-C-T		not specified	Likely benign (May 26, 2023)
1-151778894-A-T		not specified	Uncertain significance (Feb 27, 2023)
1-151778903-C-T		not specified	Uncertain significance (Aug 05, 2022)
1-151778916-T-C		not specified	Uncertain significance (Jan 12, 2024)
1-151778967-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-151778997-G-T		not specified	Uncertain significance (Dec 18, 2023)
1-151780068-T-C		not specified	Uncertain significance (Sep 25, 2023)
1-151780136-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-151781509-A-G		not specified	Uncertain significance (Oct 19, 2021)
1-151782910-C-G		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRKH	protein_coding	protein_coding	ENST00000368822	12	21310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0324	0.968	125085	0	70	125155	0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	224	314	0.713	0.0000165	3658
Missense in Polyphen		67	101.1	0.66271		1185
Synonymous	1.37	94	113	0.835	0.00000572	1108
Loss of Function	3.47	8	27.7	0.288	0.00000132	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000232	0.000232
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.000668	0.000654
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000256	0.000256
Middle Eastern	0.000668	0.000654
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the primary piRNA biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. The piRNA metabolic process 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 the final steps of primary piRNA biogenesis by participating in the processing of 31-37 nt intermediates into mature piRNAs. May act in pi-bodies and piP-bodies by transferring piRNA precursors or intermediates to or between these granules. {ECO:0000250|UniProtKB:Q80VL1}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.912
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.1

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.385
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrkh
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: male meiotic nuclear division;spermatogenesis;fertilization;cell differentiation;gene silencing by RNA;piRNA metabolic process;DNA methylation involved in gamete generation
• Cellular component: mitochondrion;pi-body;piP-body
• Molecular function: RNA binding