CCDC92

coiled-coil domain containing 92

Basic information

Region (hg38): 12:123918659-123972831

Links

ENSG00000119242 ∙ NCBI:80212 ∙ ∙ HGNC:29563 ∙ Uniprot:Q53HC0 ∙ 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 CCDC92 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC92 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in CCDC92

This is a list of pathogenic ClinVar variants found in the CCDC92 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123918688-C-T		not specified	Uncertain significance (Aug 04, 2021)
12-123918725-G-A		not specified	Uncertain significance (May 17, 2023)
12-123918730-C-A		DNAH10-related disorder	Likely benign (Jul 10, 2019)
12-123918751-G-A		Male infertility	Uncertain significance (-)
12-123918764-C-T			Uncertain significance (Feb 15, 2022)
12-123918806-C-T		not specified	Uncertain significance (Nov 01, 2023)
12-123918837-A-G			Likely benign (Jul 01, 2022)
12-123918866-C-T		not specified	Uncertain significance (Jan 26, 2022)
12-123918883-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-123918940-G-A		not specified	Uncertain significance (Jan 16, 2024)
12-123918952-G-A			Benign (Jul 20, 2018)
12-123923841-A-C		not specified	Uncertain significance (Oct 03, 2022)
12-123923849-C-A		not specified	Uncertain significance (Jun 16, 2024)
12-123924386-G-A		not specified	Uncertain significance (Aug 30, 2021)
12-123924395-C-G		not specified	Uncertain significance (Oct 02, 2023)
12-123924438-C-T		DNAH10-related disorder	Likely benign (Apr 29, 2019)
12-123925059-C-G		not specified	Uncertain significance (Oct 25, 2023)
12-123925113-C-G		not specified	Uncertain significance (Dec 14, 2021)
12-123925141-G-A		DNAH10-related disorder	Uncertain significance (Dec 14, 2023)
12-123925146-C-T		DNAH10-related disorder	Conflicting classifications of pathogenicity (Jul 11, 2023)
12-123925147-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-123925165-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-123925170-G-A		not specified	Uncertain significance (Jun 11, 2021)
12-123925198-G-A			Likely benign (Oct 24, 2017)
12-123926653-A-G		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC92	protein_coding	protein_coding	ENST00000238156	4	54172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.300	0.696	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.314	198	211	0.939	0.0000141	2138
Missense in Polyphen		77	85.767	0.89778		859
Synonymous	0.0860	101	102	0.989	0.00000790	664
Loss of Function	2.49	3	12.5	0.240	7.03e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000983	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.179
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.333
• hipred: N
• hipred_score: 0.427
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc92
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Cellular component: nucleoplasm;centrosome;centriole;intracellular membrane-bounded organelle
• Molecular function: protein binding