CCDC28B

coiled-coil domain containing 28B

Basic information

Region (hg38): 1:32200594-32205453

Links

ENSG00000160050 ∙ NCBI:79140 ∙ OMIM:610162 ∙ HGNC:28163 ∙ Uniprot:Q9BUN5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bardet-Biedl syndrome 1 (No Known Disease Relationship), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the CCDC28B gene.

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			1	2		3
missense			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	10	4	2

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)
1-32202008-C-T			Benign (Jun 09, 2021)
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)
1-32203932-C-T		not specified	Uncertain significance (May 18, 2022)
1-32203995-G-A			Uncertain significance (Nov 28, 2016)
1-32204031-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-32204044-C-T		Bardet-Biedl syndrome 1, modifier of • Bardet-Biedl syndrome	Uncertain significance; risk factor (Jan 19, 2006)
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)
1-32204316-G-A		Bardet-Biedl syndrome 1	Benign/Likely benign (Mar 29, 2022)
1-32204317-G-A		not specified	Benign/Likely benign (Dec 01, 2023)
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)
1-32205186-G-C		CCDC28B-related disorder	Likely benign (Feb 21, 2019)
1-32205429-C-T			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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