TDRD7
protein-codingtudor domain containing 7, the group of Tudor domain containing
Gene summary
The protein encoded by this gene belongs to the Tudor family of proteins. This protein contains conserved Tudor domains and LOTUS domains. It is a component of RNA granules, which function in RNA processing. Mutations in this gene have been associated with cataract formation in mouse and human. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~84.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013484
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013484
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013484
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: Ophthalmologic; Pharmacogenomic
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TDRD7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014290.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 10 | 25 | 1 | 37 | |
| missense | 1 | 180 | 14 | 1 | 196 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 5 | 1 | 6 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 7 | 3 | 190 | 39 | 2 | 241 |
Highest pathogenic variant AF is 0.0000075258754
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055105.2 | 16 | MANE Select | |
| Ensembl | ENSP00000347444.4 | 16 | MANE Select | |
| RefSeq | NP_001289813.1 | 15 | Standard | |
| Ensembl | ENSP00000531656.1 | 14 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tdrd7a | Danio rerio | Structure: primordial germ cell Quality: size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Aurora A signaling
Biological Process
- lens morphogenesis in camera-type eye
- spermatogenesis
- posttranscriptional regulation of gene expression
- lens fiber cell differentiation
Molecular Function
- mRNA binding
- protein binding
- protein N-terminus binding
Cellular Component
- cytoplasm
- mitochondrial matrix
- chromatoid body
- ribonucleoprotein granule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355295
- Coding exons
- 16
- Length
- 84176
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125748
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.988 | 503 | 569 | 0.883 | 0.0000293 | 7242 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00023 | 0.00019 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.649
- RVIS EVS
- -1.28
- RVIS percentile EVS
- 5.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.915
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |