CCDC160
Basic information
Region (hg38): X:134237047-134246842
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 CCDC160 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 | 2 | |||||
| missense | 16 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 4 | 1 |
Variants in CCDC160
This is a list of pathogenic ClinVar variants found in the CCDC160 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-134244820-A-T | Inborn genetic diseases | Uncertain significance (Jul 11, 2017) | ||
| X-134244834-A-G | not specified | Uncertain significance (Oct 30, 2023) | ||
| X-134244867-C-G | not specified | Uncertain significance (Feb 13, 2023) | ||
| X-134244907-C-T | not specified | Likely benign (Sep 12, 2023) | ||
| X-134244939-A-G | not specified | Uncertain significance (Jul 06, 2024) | ||
| X-134244972-G-C | not specified | Uncertain significance (Aug 28, 2024) | ||
| X-134244998-T-C | Likely benign (Apr 01, 2023) | |||
| X-134245080-A-G | not specified | Uncertain significance (Oct 13, 2023) | ||
| X-134245102-C-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| X-134245147-A-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| X-134245205-G-T | not specified | Uncertain significance (Sep 03, 2024) | ||
| X-134245223-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| X-134245252-A-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| X-134245262-G-A | Likely benign (Feb 01, 2023) | |||
| X-134245275-A-G | not specified | Uncertain significance (May 13, 2024) | ||
| X-134245381-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
| X-134245404-G-A | not specified | Uncertain significance (Oct 09, 2024) | ||
| X-134245507-T-G | not specified | Uncertain significance (Oct 27, 2022) | ||
| X-134245636-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| X-134245639-T-C | not specified | Likely benign (Jun 10, 2024) | ||
| X-134245653-CT-C | Benign (Sep 25, 2018) | |||
| X-134245734-ACAT-A | Uncertain significance (Jul 01, 2023) | |||
| X-134245748-C-G | not specified | Uncertain significance (Jan 19, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCDC160 | protein_coding | protein_coding | ENST00000517294 | 1 | 9161 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0170 | 0.729 | 117905 | 1 | 2 | 117908 | 0.0000127 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.139 | 89 | 85.4 | 1.04 | 0.00000585 | 2158 |
| Missense in Polyphen | 2 | 1.6463 | 1.2148 | 47 | ||
| Synonymous | -1.28 | 41 | 31.8 | 1.29 | 0.00000222 | 552 |
| Loss of Function | 0.736 | 3 | 4.73 | 0.634 | 2.98e-7 | 145 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000842 | 0.0000676 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000149 | 0.00000941 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000685 | 0.0000369 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.493
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- 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
- Ccdc160
- 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype;