CCDC90B

coiled-coil domain containing 90B

Basic information

Region (hg38): 11:83259081-83286390

Links

ENSG00000137500 ∙ NCBI:60492 ∙ ∙ HGNC:28108 ∙ Uniprot:Q9GZT6 ∙ 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 CCDC90B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC90B 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in CCDC90B

This is a list of pathogenic ClinVar variants found in the CCDC90B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-83265870-A-G		not specified	Uncertain significance (Mar 25, 2024)
11-83265877-G-T		not specified	Uncertain significance (Jul 14, 2023)
11-83265891-T-C		not specified	Uncertain significance (Oct 27, 2023)
11-83273660-T-A		not specified	Uncertain significance (Jul 19, 2023)
11-83273661-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-83273675-A-G		not specified	Uncertain significance (Jun 01, 2023)
11-83273684-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-83273804-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-83273845-C-G		not specified	Uncertain significance (Jan 31, 2024)
11-83273851-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-83273852-G-C		not specified	Uncertain significance (Nov 13, 2024)
11-83273863-T-C		not specified	Uncertain significance (Oct 20, 2024)
11-83274652-C-T		not specified	Uncertain significance (Sep 30, 2024)
11-83274671-T-G		not specified	Uncertain significance (Feb 28, 2024)
11-83274682-A-G		not specified	Uncertain significance (Sep 21, 2023)
11-83274690-G-C		not specified	Uncertain significance (Jun 16, 2024)
11-83278749-C-T		not specified	Uncertain significance (Feb 07, 2023)
11-83278782-A-C		not specified	Uncertain significance (Oct 09, 2024)
11-83278790-A-G		not specified	Uncertain significance (Oct 12, 2024)
11-83278800-C-G		not specified	Uncertain significance (Jul 13, 2021)
11-83278814-T-C		not specified	Uncertain significance (Feb 13, 2024)
11-83280143-T-A		not specified	Uncertain significance (Jul 05, 2024)
11-83280146-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-83280222-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-83280246-T-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC90B	protein_coding	protein_coding	ENST00000529689	9	27312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000993	0.803	125661	0	83	125744	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00196	128	128	1.00	0.00000599	1658
Missense in Polyphen		40	43.986	0.90938		678
Synonymous	-1.12	54	44.5	1.21	0.00000213	461
Loss of Function	1.28	10	15.4	0.648	7.15e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00246	0.00239
Ashkenazi Jewish	0.000814	0.000794
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000110	0.000109
South Asian	0.000492	0.000425
Other	0.000337	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.894
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.333
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc90b

Gene ontology

• Cellular component: mitochondrion;integral component of membrane;mitochondrial membrane
• Molecular function: protein binding