CCDC146

coiled-coil domain containing 146

Basic information

Region (hg38): 7:77122434-77329533

Links

ENSG00000135205 ∙ NCBI:57639 ∙ OMIM:619829 ∙ HGNC:29296 ∙ Uniprot:Q8IYE0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 94	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	38441556

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC146 gene.

• not_specified (133 variants)
• not_provided (2 variants)
• Male_infertility_due_to_sperm_motility_disorder (2 variants)
• Male_infertility_with_spermatogenesis_disorder_due_to_single_gene_mutation (2 variants)
• Spermatogenic_failure_94 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC146 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020879.3. 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				1		1
missense	1		106	4		111
nonsense	1					1
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)						0
Total	3	0	106	5	0

Highest pathogenic variant AF is 0.0000582488

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC146	protein_coding	protein_coding	ENST00000285871	18	207100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-26	0.00720	125451	3	294	125748	0.00118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.878	425	479	0.887	0.0000247	6346
Missense in Polyphen		68	89.145	0.7628		1231
Synonymous	-0.736	182	170	1.07	0.00000876	1634
Loss of Function	1.11	45	53.8	0.836	0.00000302	676

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00215	0.00214
Ashkenazi Jewish	0.00675	0.00667
East Asian	0.00192	0.00190
Finnish	0.000185	0.000139
European (Non-Finnish)	0.000658	0.000642
Middle Eastern	0.00192	0.00190
South Asian	0.00179	0.00170
Other	0.00115	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.620
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.74

Haploinsufficiency Scores

• pHI: 0.0501
• hipred: N
• hipred_score: 0.197
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc146

Gene ontology

• Cellular component: centriole