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.

• not_specified (63 variants)

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. These statistics are base on transcript: NM_000052848.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			62	1		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	1	0

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