CCDC169

coiled-coil domain containing 169

Basic information

Region (hg38): 13:36222008-36297840

Previous symbols: [ "C13orf38" ]

Links

ENSG00000242715 ∙ NCBI:728591 ∙ ∙ HGNC:34361 ∙ Uniprot:A6NNP5 ∙ 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 CCDC169 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC169 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	5	0	0

Variants in CCDC169

This is a list of pathogenic ClinVar variants found in the CCDC169 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-36227206-T-C		not specified	Uncertain significance (Mar 07, 2023)
13-36227263-A-T		not specified	Uncertain significance (Aug 12, 2024)
13-36283685-G-A		not specified	Uncertain significance (Feb 28, 2023)
13-36295796-G-A		not specified	Uncertain significance (Mar 05, 2024)
13-36295828-A-G		not specified	Uncertain significance (Mar 15, 2024)
13-36295837-A-G		not specified	Uncertain significance (Oct 16, 2024)
13-36297659-A-C		not specified	Uncertain significance (Mar 25, 2024)
13-36297697-T-C		not specified	Uncertain significance (Dec 01, 2022)
13-36297700-T-C		not specified	Uncertain significance (Dec 15, 2022)
13-36297706-C-A		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC169	protein_coding	protein_coding	ENST00000503173	8	70796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000379	0.606	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	102	112	0.911	0.00000572	1559
Missense in Polyphen		29	34.68	0.83622		532
Synonymous	0.721	34	39.8	0.855	0.00000191	424
Loss of Function	0.906	10	13.6	0.735	7.54e-7	177

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: 0.88
• rvis_percentile_EVS: 88.96

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc169