TDRD10

tudor domain containing 10, the group of RNA binding motif containing|Tudor domain containing

Basic information

Region (hg38): 1:154502218-154548147

Links

ENSG00000163239 ∙ NCBI:126668 ∙ ∙ HGNC:25316 ∙ Uniprot:Q5VZ19 ∙ 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 TDRD10 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD10 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in TDRD10

This is a list of pathogenic ClinVar variants found in the TDRD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-154507260-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-154521343-G-C		not specified	Uncertain significance (Dec 06, 2022)
1-154542774-G-C		not specified	Uncertain significance (Nov 10, 2022)
1-154542797-T-C		not specified	Uncertain significance (Oct 17, 2023)
1-154544036-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-154544081-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-154544387-A-G		not specified	Uncertain significance (Sep 27, 2022)
1-154544429-C-G		not specified	Uncertain significance (Dec 03, 2021)
1-154544456-A-T		not specified	Uncertain significance (Feb 22, 2023)
1-154544460-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-154544462-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-154544895-A-G		not specified	Uncertain significance (Jul 27, 2022)
1-154547426-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-154547433-T-C		not specified	Uncertain significance (Oct 18, 2021)
1-154547439-G-A		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD10	protein_coding	protein_coding	ENST00000368480	11	45929

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000115	0.951	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	171	212	0.806	0.0000117	2387
Missense in Polyphen		40	60.552	0.66058		681
Synonymous	0.329	86	90.0	0.956	0.00000568	732
Loss of Function	1.83	11	19.8	0.556	9.80e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.000110	0.000109
South Asian	0.0000980	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.220
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Gene ontology

• Molecular function: RNA binding