CCDC28B
Basic information
Region (hg38): 1:32200595-32205453
Links
Phenotypes
GenCC
Source:
- Bardet-Biedl syndrome 1 (No Known Disease Relationship), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Bardet-Biedl syndrome, modifier of | AD | General | Variants are described as related to modifying alleles, with little evidence that the variant would cause disease alone | General | 12677556; 16327777; 22773737 |
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 CCDC28B 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 | 3 | |||||
missense | 16 | 18 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 0 | 0 | 17 | 3 | 3 |
Variants in CCDC28B
This is a list of pathogenic ClinVar variants found in the CCDC28B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-32201991-A-C | not specified | Uncertain significance (May 02, 2024) | ||
1-32201994-C-T | not specified | Uncertain significance (Nov 22, 2024) | ||
1-32202008-C-T | Benign (Jun 09, 2021) | |||
1-32202032-C-A | Bardet-Biedl syndrome 1 | Uncertain significance (May 10, 2024) | ||
1-32202098-A-G | Uncertain significance (May 01, 2024) | |||
1-32203676-C-A | Benign (Nov 10, 2018) | |||
1-32203889-G-C | not specified | Uncertain significance (Oct 16, 2023) | ||
1-32203931-G-C | not specified | Uncertain significance (Dec 25, 2024) | ||
1-32203932-C-T | not specified | Uncertain significance (May 18, 2022) | ||
1-32203995-G-A | Uncertain significance (Nov 28, 2016) | |||
1-32204013-A-G | not specified | Uncertain significance (Aug 19, 2024) | ||
1-32204030-C-T | not specified | Uncertain significance (Nov 21, 2024) | ||
1-32204031-G-A | not specified | Uncertain significance (Aug 17, 2021) | ||
1-32204044-C-T | Bardet-Biedl syndrome 1, modifier of • Bardet-Biedl syndrome • CCDC28B-related disorder | Uncertain significance (Apr 19, 2023) | ||
1-32204186-G-A | not specified | Uncertain significance (Aug 15, 2023) | ||
1-32204190-G-A | Uncertain significance (Mar 06, 2013) | |||
1-32204246-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
1-32204281-G-A | not specified | Uncertain significance (Aug 06, 2024) | ||
1-32204291-A-G | not specified | Uncertain significance (Sep 20, 2024) | ||
1-32204309-T-C | not specified | Uncertain significance (Feb 14, 2025) | ||
1-32204316-G-A | Bardet-Biedl syndrome 1 | Benign/Likely benign (Mar 29, 2022) | ||
1-32204317-G-A | not specified | Benign/Likely benign (Dec 01, 2024) | ||
1-32204332-C-A | not specified | Uncertain significance (Dec 13, 2022) | ||
1-32204354-G-A | not specified | Uncertain significance (Jul 06, 2022) | ||
1-32204735-T-G | Likely benign (Jun 01, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CCDC28B | protein_coding | protein_coding | ENST00000373602 | 5 | 5002 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.23e-9 | 0.0262 | 125712 | 0 | 28 | 125740 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.03 | 83 | 114 | 0.729 | 0.00000668 | 1287 |
Missense in Polyphen | 23 | 35.273 | 0.65205 | 418 | ||
Synonymous | 0.133 | 48 | 49.2 | 0.976 | 0.00000294 | 403 |
Loss of Function | -1.18 | 11 | 7.51 | 1.46 | 3.17e-7 | 103 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.000443 | 0.000397 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000159 | 0.000149 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000167 | 0.000163 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in ciliogenesis. Regulates cilia length through its interaction with MAPKAP1/SIN1 but independently of mTORC2 complex. Modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation. Does not seem to modulate assembly and function of mTORC1 complex. {ECO:0000269|PubMed:23015189, ECO:0000269|PubMed:23727834}.;
- Disease
- DISEASE: Bardet-Biedl syndrome (BBS) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:16327777}. Note=The gene represented in this entry acts as a disease modifier.;
Recessive Scores
- pRec
- 0.183
Intolerance Scores
- loftool
- 0.783
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.06
Haploinsufficiency Scores
- pHI
- 0.171
- hipred
- N
- hipred_score
- 0.208
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0312
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccdc28b
- Phenotype
Zebrafish Information Network
- Gene name
- ccdc28b
- Affected structure
- cell
- Phenotype tag
- abnormal
- Phenotype quality
- detached from
Gene ontology
- Biological process
- cilium assembly
- Cellular component
- cytoplasm;centrosome
- Molecular function
- protein binding