CCDC9B

coiled-coil domain containing 9B

Basic information

Region (hg38): 15:40331452-40340939

Previous symbols: [ "C15orf52" ]

Links

ENSG00000188549 ∙ NCBI:388115 ∙ ∙ HGNC:33488 ∙ Uniprot:Q6ZUT6 ∙ 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 CCDC9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC9B 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		1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in CCDC9B

This is a list of pathogenic ClinVar variants found in the CCDC9B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40335246-C-T		not specified	Uncertain significance (Aug 02, 2021)
15-40335349-C-T		not specified	Uncertain significance (Oct 06, 2021)
15-40336778-A-T		not specified	Uncertain significance (Nov 12, 2021)
15-40339542-G-A			Likely benign (Aug 01, 2022)
15-40340815-T-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC9B	protein_coding	protein_coding	ENST00000559313	11	9516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-13	0.173	125621	1	119	125741	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.577	344	315	1.09	0.0000190	3361
Missense in Polyphen		121	102.62	1.1791		1109
Synonymous	-0.303	127	123	1.03	0.00000748	1107
Loss of Function	0.960	23	28.5	0.806	0.00000146	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000499	0.000483
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000210	0.000202
Middle Eastern	0.000115	0.000109
South Asian	0.00263	0.00262
Other	0.000826	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0819

Intolerance Scores

• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.23

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.233
• ghis: 0.455

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccdc9b

Gene ontology

• Molecular function: RNA binding