TDRD7

tudor domain containing 7, the group of Tudor domain containing

Basic information

Region (hg38): 9:97412096-97496125

Links

ENSG00000196116

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

Phenotypes

GenCC

Source: genCC

cataract 36 (Moderate), 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 (2 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. These statistics are base on transcript: . Only rare variants are included in the table.

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 clinvar	11 clinvar	4 clinvar	25
missense			112 clinvar	8 clinvar	2 clinvar	122
nonsense	1 clinvar					1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	2	0	122	19	6

Loading clinvar variants...

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