CCDC96

coiled-coil domain containing 96

Basic information

Region (hg38): 4:7040848-7043001

Links

ENSG00000173013 ∙ NCBI:257236 ∙ OMIM:619347 ∙ HGNC:26900 ∙ Uniprot:Q2M329 ∙ 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 CCDC96 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC96 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			42	1		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	0

Variants in CCDC96

This is a list of pathogenic ClinVar variants found in the CCDC96 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-7041315-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-7041342-C-T		not specified	Uncertain significance (Feb 27, 2024)
4-7041409-G-C		not specified	Uncertain significance (Mar 01, 2023)
4-7041414-G-A		not specified	Uncertain significance (Aug 11, 2022)
4-7041414-G-C		not specified	Uncertain significance (Sep 10, 2024)
4-7041432-C-T		not specified	Uncertain significance (Nov 09, 2021)
4-7041470-G-A		not specified	Uncertain significance (Sep 21, 2023)
4-7041495-T-G		not specified	Uncertain significance (Feb 15, 2023)
4-7041506-A-C		not specified	Uncertain significance (Oct 09, 2024)
4-7041509-A-T		not specified	Uncertain significance (Nov 18, 2022)
4-7041602-A-C		not specified	Uncertain significance (Mar 25, 2024)
4-7041641-C-T		not specified	Uncertain significance (Sep 27, 2024)
4-7041719-T-C		not specified	Uncertain significance (Mar 01, 2023)
4-7041790-C-A		not specified	Uncertain significance (Aug 21, 2024)
4-7041812-C-A		not specified	Uncertain significance (Sep 01, 2021)
4-7041819-C-G		not specified	Uncertain significance (Sep 19, 2022)
4-7041827-T-A		not specified	Uncertain significance (Jan 03, 2024)
4-7041843-C-T		not specified	Uncertain significance (May 20, 2024)
4-7041893-C-G		not specified	Uncertain significance (Jul 19, 2023)
4-7041912-C-T		not specified	Uncertain significance (Sep 04, 2024)
4-7041913-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-7041953-C-T		not specified	Uncertain significance (Sep 10, 2024)
4-7042032-G-C		not specified	Likely benign (Oct 01, 2024)
4-7042116-C-A		not specified	Uncertain significance (Feb 15, 2023)
4-7042128-G-A		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC96	protein_coding	protein_coding	ENST00000310085	1	2150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-17	0.000996	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.188	310	301	1.03	0.0000175	3548
Missense in Polyphen		86	73.864	1.1643		900
Synonymous	-0.324	138	133	1.04	0.00000778	1095
Loss of Function	-0.951	23	18.6	1.24	0.00000109	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.0843
• hipred: N
• hipred_score: 0.238
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc96

Gene ontology

• Cellular component: cytoplasm;microtubule organizing center