CCDC97

coiled-coil domain containing 97

Basic information

Region (hg38): 19:41310172-41324873

Links

ENSG00000142039 ∙ NCBI:90324 ∙ ∙ HGNC:28289 ∙ Uniprot:Q96F63 ∙ 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 CCDC97 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC97 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in CCDC97

This is a list of pathogenic ClinVar variants found in the CCDC97 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41316524-G-T		not specified	Uncertain significance (Sep 14, 2023)
19-41316665-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-41316684-G-A		not specified	Uncertain significance (Mar 11, 2024)
19-41316684-G-T		not specified	Uncertain significance (May 15, 2024)
19-41316705-T-A		not specified	Uncertain significance (Feb 06, 2023)
19-41316717-G-A		not specified	Uncertain significance (Jan 08, 2024)
19-41316728-C-A		not specified	Uncertain significance (Nov 03, 2023)
19-41316729-G-A		not specified	Uncertain significance (Feb 17, 2024)
19-41316732-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-41316759-G-A		not specified	Likely benign (Mar 28, 2022)
19-41316773-C-T		not specified	Uncertain significance (Mar 17, 2023)
19-41316806-C-T		not specified	Uncertain significance (May 27, 2022)
19-41319579-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-41319615-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-41319691-C-A		not specified	Uncertain significance (Aug 26, 2022)
19-41319711-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-41319726-C-T		not specified	Uncertain significance (Apr 01, 2022)
19-41319756-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-41319838-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-41320376-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-41320379-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-41320388-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-41320416-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-41320433-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-41320434-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC97	protein_coding	protein_coding	ENST00000269967	5	14695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-9	0.123	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.776	200	233	0.857	0.0000159	2215
Missense in Polyphen		98	103.92	0.943		913
Synonymous	-0.383	101	96.2	1.05	0.00000632	691
Loss of Function	0.210	14	14.9	0.941	8.00e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000556	0.000538
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.000419	0.000370
European (Non-Finnish)	0.000396	0.000387
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.197
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc97