CTDNEP1
Basic information
Region (hg38): 17:7243591-7252491
Previous symbols: [ "DULLARD" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDNEP1 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in CTDNEP1
This is a list of pathogenic ClinVar variants found in the CTDNEP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-7246814-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 17-7247096-G-A | not specified | Uncertain significance (Mar 08, 2024) | ||
| 17-7251218-G-A | not specified | Uncertain significance (Apr 01, 2024) | ||
| 17-7251258-G-C | not specified | Uncertain significance (Mar 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTDNEP1 | protein_coding | protein_coding | ENST00000573600 | 8 | 8901 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.975 | 0.0253 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.54 | 56 | 141 | 0.398 | 0.00000755 | 1591 |
| Missense in Polyphen | 17 | 59.329 | 0.28654 | 717 | ||
| Synonymous | -1.03 | 64 | 54.4 | 1.18 | 0.00000282 | 479 |
| Loss of Function | 3.12 | 0 | 11.3 | 0.00 | 4.82e-7 | 132 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine protein phosphatase forming with CNEP1R1 an active phosphatase complex that dephosphorylates and may activate LPIN1 and LPIN2. LPIN1 and LPIN2 are phosphatidate phosphatases that catalyze the conversion of phosphatidic acid to diacylglycerol and control the metabolism of fatty acids at different levels. May indirectly modulate the lipid composition of nuclear and/or endoplasmic reticulum membranes and be required for proper nuclear membrane morphology and/or dynamics. May also indirectly regulate the production of lipid droplets and triacylglycerol. May antagonize BMP signaling. {ECO:0000269|PubMed:17420445, ECO:0000269|PubMed:22134922}.;
- Pathway
- TGF-Ncore;Depolymerisation of the Nuclear Lamina;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.504
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.456
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctdnep1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype; renal/urinary system phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- ctdnep1b
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- protein dephosphorylation;nuclear envelope organization;mitotic nuclear envelope disassembly;gamete generation;mesoderm development;positive regulation of triglyceride biosynthetic process;protein localization to nucleus;positive regulation of canonical Wnt signaling pathway
- Cellular component
- nuclear envelope;cytoplasm;endoplasmic reticulum membrane;lipid droplet;integral component of membrane;nuclear membrane;Nem1-Spo7 phosphatase complex
- Molecular function
- phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;protein binding