TDRD6

tudor domain containing 6, the group of Tudor domain containing

Basic information

Region (hg38): 6:46687874-46704319

Links

ENSG00000180113 ∙ NCBI:221400 ∙ OMIM:611200 ∙ HGNC:21339 ∙ Uniprot:O60522 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR
• schizophrenia (Limited), mode of inheritance: AD
• oligospermia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TDRD6 gene.

• Inborn genetic diseases (103 variants)
• not provided (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD6 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				7		7
missense			102	6	3	111
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	103	13	3

Variants in TDRD6

This is a list of pathogenic ClinVar variants found in the TDRD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46688136-C-T		not specified	Uncertain significance (Jun 16, 2023)
6-46688188-C-G		not specified	Uncertain significance (Jun 26, 2023)
6-46688214-C-T		not specified	Uncertain significance (Jul 21, 2021)
6-46688220-A-C		not specified	Uncertain significance (Jan 02, 2024)
6-46688255-T-A		not specified	Uncertain significance (Jul 25, 2023)
6-46688262-G-A		not specified	Uncertain significance (Aug 02, 2022)
6-46688322-C-T		not specified	Uncertain significance (Jul 19, 2022)
6-46688331-C-T		not specified	Uncertain significance (May 18, 2022)
6-46688342-C-G		not specified	Uncertain significance (Dec 13, 2021)
6-46688347-C-T			Likely benign (Dec 12, 2017)
6-46688371-G-T		not specified	Uncertain significance (Sep 21, 2023)
6-46688445-C-T		not specified	Uncertain significance (Oct 20, 2021)
6-46688460-C-T		not specified	Uncertain significance (Sep 01, 2021)
6-46688480-G-A		not specified	Uncertain significance (Feb 01, 2023)
6-46688495-C-T		not specified	Uncertain significance (Oct 12, 2022)
6-46688538-C-A		not specified	Uncertain significance (Feb 28, 2024)
6-46688579-C-T			Uncertain significance (Aug 01, 2023)
6-46688604-G-A		not specified	Uncertain significance (Sep 22, 2023)
6-46688622-A-T		not specified	Uncertain significance (Jun 07, 2023)
6-46688645-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-46688735-A-T		not specified	Uncertain significance (Feb 07, 2023)
6-46688744-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-46688770-A-G			Likely benign (Jun 01, 2022)
6-46688813-C-G		not specified	Uncertain significance (Feb 27, 2024)
6-46688821-G-A			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD6	protein_coding	protein_coding	ENST00000316081	4	16445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.44e-45	3.76e-7	125209	0	539	125748	0.00215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.28	1302	1.09e+3	1.19	0.0000579	13671
Missense in Polyphen		346	301.48	1.1477		3797
Synonymous	-1.53	469	429	1.09	0.0000246	4061
Loss of Function	0.0476	68	68.4	0.994	0.00000333	956

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00268	0.00253
Ashkenazi Jewish	0.000996	0.000993
East Asian	0.00114	0.00114
Finnish	0.00729	0.00519
European (Non-Finnish)	0.00249	0.00242
Middle Eastern	0.00114	0.00114
South Asian	0.00156	0.00154
Other	0.00215	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in spermiogenesis, chromatoid body formation and for proper precursor and mature miRNA expression. {ECO:0000250|UniProtKB:P61407}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.991
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.08

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.123
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrd6
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: cytoplasm;chromatoid body