TDRD7

tudor domain containing 7, the group of Tudor domain containing

Basic information

Region (hg38): 9:97412095-97496125

Links

ENSG00000196116 ∙ NCBI:23424 ∙ OMIM:611258 ∙ HGNC:30831 ∙ Uniprot:Q8NHU6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 36 (Limited), mode of inheritance: AR
• cataract 36 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 36	AR	Ophthalmologic; Pharmacogenomic	Some affected individuals have been described as developing open-angle glaucoma with increased intraocular pressure following cataract extraction; Agents that may contribute to glaucoma should be avoided	Ophthalmologic	21436445

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TDRD7 gene.

• Cataract 36 (108 variants)
• not provided (47 variants)
• Inborn genetic diseases (40 variants)
• not specified (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDRD7 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			10	11	4	25
missense			80	3	2	85
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	1	1	1	4
non coding			13	15	23	51
Total	2	0	103	29	29

Variants in TDRD7

This is a list of pathogenic ClinVar variants found in the TDRD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-97412098-G-T		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97412112-C-G		Cataract 36	Benign (Jan 13, 2018)
9-97412123-T-C		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97412125-C-G		Cataract 36	Uncertain significance (Apr 27, 2017)
9-97412162-G-C		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97412181-A-G		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97412198-G-A		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97412203-G-C		Cataract 36	Uncertain significance (Jan 12, 2018)
9-97428457-T-C		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97428498-A-G		not specified • Cataract 36	Benign (Jan 27, 2024)
9-97428519-T-C		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97428654-G-C		Cataract 36 • Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
9-97428662-G-C		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
9-97428664-T-C		Cataract 36	Uncertain significance (Jan 12, 2018)
9-97428684-A-C		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97428690-C-T		not specified • Cataract 36	Benign (Jan 18, 2024)
9-97428691-G-A		not specified • Cataract 36	Benign (Jan 15, 2024)
9-97428841-T-C			Benign (Jun 29, 2018)
9-97430704-T-C			Benign (Jun 28, 2018)
9-97430719-A-G			Benign (Jun 29, 2018)
9-97430831-T-C			Benign (Jun 29, 2018)
9-97430948-A-G		Cataract 36	Uncertain significance (Jan 13, 2018)
9-97430956-C-T		Cataract 36	Conflicting classifications of pathogenicity (Aug 17, 2023)
9-97431020-C-T		Cataract 36	Uncertain significance (Aug 25, 2021)
9-97431021-G-A			Uncertain significance (Mar 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDRD7	protein_coding	protein_coding	ENST00000355295	16	84176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000611	0.999	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.988	503	569	0.883	0.0000293	7242
Missense in Polyphen		136	191.13	0.71155		2548
Synonymous	0.265	200	205	0.976	0.0000111	2079
Loss of Function	4.41	15	47.9	0.313	0.00000242	630

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000390	0.000389
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000232	0.000193
Middle Eastern	0.0000544	0.0000544
South Asian	0.000297	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. Required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. Also required during spermatogenesis. {ECO:0000269|PubMed:21436445}.
• Disease: DISEASE: Cataract 36 (CTRCT36) [MIM:613887]: An opacification of the crystalline lens of the eye becoming evident at birth. It frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269|PubMed:21436445}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Aurora A signaling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.649
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.17

Haploinsufficiency Scores

• pHI: 0.242
• hipred: N
• hipred_score: 0.415
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdrd7
• Phenotype: reproductive system phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: tdrd7a
• Affected structure: primordial germ cell
• Phenotype tag: abnormal
• Phenotype quality: size

Gene ontology

• Biological process: lens morphogenesis in camera-type eye;spermatogenesis;posttranscriptional regulation of gene expression;lens fiber cell differentiation
• Cellular component: cytoplasm;mitochondrial matrix;chromatoid body;ribonucleoprotein granule
• Molecular function: mRNA binding;protein binding;protein N-terminus binding