CCDC83

coiled-coil domain containing 83

Basic information

Region (hg38): 11:85855101-85920021

Links

ENSG00000150676 ∙ NCBI:220047 ∙ ∙ HGNC:28535 ∙ Uniprot:Q8IWF9 ∙ 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 CCDC83 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC83 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	20	2	0

Variants in CCDC83

This is a list of pathogenic ClinVar variants found in the CCDC83 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-85873238-G-C		not specified	Uncertain significance (Oct 05, 2023)
11-85873279-A-G		not specified	Uncertain significance (Sep 13, 2023)
11-85882520-G-A		not specified	Uncertain significance (Apr 23, 2024)
11-85882556-T-C		not specified	Uncertain significance (May 11, 2022)
11-85882572-T-A		not specified	Uncertain significance (Jan 10, 2023)
11-85882581-G-T		not specified	Uncertain significance (Apr 12, 2023)
11-85886209-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-85886210-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-85886238-C-T		not specified	Uncertain significance (Jan 09, 2024)
11-85886302-C-T		not specified	Uncertain significance (Jun 30, 2023)
11-85886326-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-85895320-C-A		not specified	Uncertain significance (May 26, 2024)
11-85895360-C-T			Likely benign (Feb 01, 2023)
11-85911315-A-G		not specified	Uncertain significance (Mar 16, 2022)
11-85911324-T-C		not specified	Uncertain significance (Jun 11, 2021)
11-85911353-C-T		not specified	Uncertain significance (Apr 20, 2024)
11-85912671-C-G		not specified	Uncertain significance (Jun 06, 2023)
11-85912696-T-C		not specified	Uncertain significance (Dec 07, 2021)
11-85915460-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-85916074-G-C		not specified	Uncertain significance (Mar 25, 2024)
11-85916085-C-T		not specified	Likely benign (Oct 13, 2023)
11-85916106-A-C		not specified	Uncertain significance (Mar 16, 2022)
11-85916129-G-A		not specified	Uncertain significance (Nov 30, 2022)
11-85919352-T-C		not specified	Uncertain significance (May 18, 2023)
11-85919409-C-G		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC83	protein_coding	protein_coding	ENST00000280245	11	64921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-9	0.541	125699	0	40	125739	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.453	239	220	1.09	0.0000104	2954
Missense in Polyphen		72	61.301	1.1745		959
Synonymous	0.133	73	74.5	0.980	0.00000345	740
Loss of Function	1.18	17	23.1	0.734	0.00000107	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000306	0.000306
Ashkenazi Jewish	0.00	0.00
East Asian	0.000123	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000226	0.000220
Middle Eastern	0.000123	0.000109
South Asian	0.000115	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0778

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.23

Haploinsufficiency Scores

• pHI: 0.0282
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc83