CCDC107

coiled-coil domain containing 107

Basic information

Region (hg38): 9:35658289-35661511

Links

ENSG00000159884 ∙ NCBI:203260 ∙ ∙ HGNC:28465 ∙ Uniprot:Q8WV48 ∙ 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 CCDC107 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC107 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	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	25	2	1

Variants in CCDC107

This is a list of pathogenic ClinVar variants found in the CCDC107 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35658334-A-G			Benign (Jul 07, 2018)
9-35658386-G-A		not specified	Likely benign (Nov 22, 2021)
9-35658416-C-A		not specified	Uncertain significance (Feb 28, 2023)
9-35658425-G-C		not specified	Uncertain significance (Nov 08, 2022)
9-35658426-T-C		not specified	Uncertain significance (Aug 23, 2021)
9-35658621-G-A		not specified	Uncertain significance (Aug 16, 2021)
9-35658623-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-35658642-G-C		not specified	Uncertain significance (Sep 22, 2023)
9-35658675-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-35658677-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-35658677-G-T		not specified	Uncertain significance (Apr 05, 2023)
9-35658680-C-G		not specified	Uncertain significance (Feb 08, 2023)
9-35660573-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-35660580-C-G		not specified	Uncertain significance (Nov 18, 2022)
9-35660590-C-G		not specified	Uncertain significance (Sep 15, 2021)
9-35660643-G-A		not specified	Uncertain significance (Aug 14, 2023)
9-35660646-C-T		not specified	Uncertain significance (Jul 14, 2021)
9-35660753-A-G		not specified	Uncertain significance (Jun 16, 2023)
9-35660756-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-35660801-A-G		not specified	Uncertain significance (Apr 17, 2024)
9-35660823-G-T		not specified	Uncertain significance (Apr 22, 2024)
9-35660826-A-G		not specified	Uncertain significance (Dec 06, 2022)
9-35660838-A-C		not specified	Uncertain significance (Nov 08, 2021)
9-35660842-G-A		not specified	Uncertain significance (Aug 04, 2023)
9-35660843-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC107	protein_coding	protein_coding	ENST00000426546	5	3208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.35e-9	0.0738	125606	0	142	125748	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	139	146	0.955	0.00000760	1760
Missense in Polyphen		52	55.933	0.92968		715
Synonymous	0.250	62	64.6	0.960	0.00000365	610
Loss of Function	-0.290	12	11.0	1.09	4.70e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00586	0.00587
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000359	0.000359
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0482

Intolerance Scores

• loftool: 0.865
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.00702
• hipred: N
• hipred_score: 0.123
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc107

Gene ontology

• Cellular component: integral component of membrane