CC2D2B

coiled-coil and C2 domain containing 2B

Basic information

Region (hg38): 10:95907602-96033745

Previous symbols: [ "C10orf130", "C10orf131" ]

Links

ENSG00000188649 ∙ NCBI:387707 ∙ ∙ HGNC:31666 ∙ Uniprot:Q6DHV5 ∙ 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 CC2D2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CC2D2B 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		3
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	4	0

Variants in CC2D2B

This is a list of pathogenic ClinVar variants found in the CC2D2B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-95927261-T-C			Likely benign (Mar 01, 2022)
10-95938065-G-C		not specified	Likely benign (Aug 12, 2021)
10-95961859-G-A			Likely benign (Jul 01, 2023)
10-95982023-C-T			Likely benign (May 01, 2022)
10-96009850-G-T		not specified	Uncertain significance (Feb 21, 2024)
10-96009918-T-C		not specified	Uncertain significance (Jul 12, 2022)
10-96012605-G-A		not specified	Uncertain significance (May 04, 2023)
10-96013794-A-T		not specified	Uncertain significance (May 06, 2022)
10-96013834-C-A		not specified	Uncertain significance (Mar 16, 2024)
10-96013852-G-C		not specified	Uncertain significance (Dec 06, 2022)
10-96016207-A-G		not specified	Uncertain significance (Dec 20, 2023)
10-96016220-T-C		not specified	Uncertain significance (Feb 02, 2024)
10-96016286-T-C		not specified	Uncertain significance (Mar 22, 2023)
10-96016301-C-T		not specified	Uncertain significance (Jul 06, 2021)
10-96019218-G-A		not specified	Uncertain significance (Jun 26, 2023)
10-96019219-T-C		not specified	Uncertain significance (Dec 08, 2023)
10-96019258-C-G		not specified	Uncertain significance (Apr 11, 2023)
10-96019269-C-A		not specified	Uncertain significance (Oct 13, 2023)
10-96019715-T-G		not specified	Uncertain significance (Jun 28, 2023)
10-96019732-C-A		not specified	Uncertain significance (Jun 22, 2024)
10-96019747-T-C		not specified	Uncertain significance (Jun 16, 2024)
10-96024866-T-C		not specified	Uncertain significance (Sep 20, 2023)
10-96024868-T-G		not specified	Uncertain significance (Jun 14, 2024)
10-96024889-A-T		not specified	Uncertain significance (Aug 04, 2023)
10-96027250-G-A		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CC2D2B	protein_coding	protein_coding	ENST00000410012	10	58656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.91e-8	0.892	124652	0	124	124776	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	147	198	0.743	0.00000924	2667
Missense in Polyphen		49	63.144	0.776		862
Synonymous	1.15	56	68.1	0.823	0.00000344	704
Loss of Function	1.69	15	23.9	0.627	0.00000130	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00253	0.00253
Ashkenazi Jewish	0.000208	0.000199
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000150
Middle Eastern	0.00	0.00
South Asian	0.00208	0.00196
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.671
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.440
• hipred: N
• hipred_score: 0.146
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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