CCDC12
Basic information
Region (hg38): 3:46916634-46982010
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 CCDC12 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 | 8 | |||||
nonsense | 0 | |||||
start loss | 1 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 8 | 1 | 0 |
Variants in CCDC12
This is a list of pathogenic ClinVar variants found in the CCDC12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-46922071-A-G | not specified | Uncertain significance (Mar 21, 2023) | ||
3-46922265-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
3-46922297-A-T | not specified | Uncertain significance (Sep 12, 2023) | ||
3-46923616-G-C | not specified | Uncertain significance (Mar 17, 2023) | ||
3-46923627-C-T | not specified | Uncertain significance (Jan 10, 2022) | ||
3-46925534-C-G | not specified | Uncertain significance (Oct 26, 2022) | ||
3-46976699-C-G | not specified | Uncertain significance (Nov 13, 2023) | ||
3-46976723-T-C | not specified | Likely benign (Feb 05, 2024) | ||
3-46976725-G-A | not specified | Uncertain significance (Feb 06, 2023) | ||
3-46976732-T-A | not specified | Uncertain significance (Sep 29, 2022) | ||
3-46976753-C-G | not specified | Uncertain significance (Aug 26, 2022) | ||
3-46979345-A-T | Benign (Jun 19, 2021) | |||
3-46979533-A-G | Benign (Jun 19, 2021) | |||
3-46979634-A-G | Benign (Jun 19, 2021) | |||
3-46979684-G-A | Gray platelet syndrome | Uncertain significance (Jan 13, 2018) | ||
3-46979700-C-T | Gray platelet syndrome | Uncertain significance (Jan 12, 2018) | ||
3-46979742-C-G | Gray platelet syndrome | Uncertain significance (Apr 06, 2018) | ||
3-46979786-G-A | Gray platelet syndrome | Uncertain significance (Jan 13, 2018) | ||
3-46979842-G-GGCCGGA | Gray platelet syndrome | Uncertain significance (Jun 14, 2016) | ||
3-46979898-C-T | Gray platelet syndrome | Uncertain significance (Oct 09, 2023) | ||
3-46979900-C-T | Likely benign (Jun 15, 2018) | |||
3-46979923-C-T | Gray platelet syndrome | Uncertain significance (Jan 13, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CCDC12 | protein_coding | protein_coding | ENST00000425441 | 7 | 60285 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0401 | 0.933 | 125508 | 2 | 238 | 125748 | 0.000955 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.418 | 89 | 101 | 0.883 | 0.00000555 | 1136 |
Missense in Polyphen | 25 | 32.794 | 0.76234 | 371 | ||
Synonymous | -0.120 | 43 | 42.0 | 1.02 | 0.00000249 | 336 |
Loss of Function | 1.91 | 4 | 10.8 | 0.371 | 5.56e-7 | 136 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0171 | 0.0134 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000134 | 0.000109 |
Finnish | 0.0000523 | 0.0000462 |
European (Non-Finnish) | 0.0000504 | 0.0000439 |
Middle Eastern | 0.000134 | 0.000109 |
South Asian | 0.000158 | 0.000131 |
Other | 0.000187 | 0.000163 |
dbNSFP
Source:
- Pathway
- Spliceosome - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- loftool
- 0.197
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.49
Haploinsufficiency Scores
- pHI
- 0.0857
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.497
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.583
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccdc12
- Phenotype
Gene ontology
- Biological process
- Cellular component
- Molecular function
- protein binding