CCDC28A

coiled-coil domain containing 28A

Basic information

Region (hg38): 6:138773769-138793319

Previous symbols: [ "C6orf80" ]

Links

ENSG00000024862 ∙ NCBI:25901 ∙ OMIM:615353 ∙ HGNC:21098 ∙ Uniprot:Q8IWP9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC28A gene.

• not_specified (15 variants)
• Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC28A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015439.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC28A	protein_coding	protein_coding	ENST00000332797	6	19800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.65e-10	0.0514	125684	0	62	125746	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0998	149	146	1.02	0.00000698	1761
Missense in Polyphen		40	52.617	0.76022		681
Synonymous	-0.657	65	58.6	1.11	0.00000281	542
Loss of Function	-0.227	14	13.1	1.07	6.35e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000828	0.000828
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.0000983	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving CCDC28A has been identified in acute leukemias. Translocation t(6;11)(q24.1;p15.5) with NUP98. The chimeric transcript is an in-frame fusion of NUP98 exon 13 to CCDC28A exon 2. Ectopic expression of NUP98-CCDC28A in mouse promotes the proliferative capacity and self-renewal potential of hematopoietic progenitors and rapidly induced fatal myeloproliferative neoplasms and defects in the differentiation of the erythro-megakaryocytic lineage. {ECO:0000269|PubMed:16028218}.

Recessive Scores

• pRec: 0.0770

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0476
• hipred: N
• hipred_score: 0.161
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc28a

Gene ontology

• Molecular function: protein binding