CCIN

calicin, the group of BTB domain containing

Basic information

Region (hg38): 9:36169388-36171334

Links

ENSG00000185972 ∙ NCBI:881 ∙ OMIM:603960 ∙ HGNC:1568 ∙ Uniprot:Q13939 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 91	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	31985809; 36527329; 36546111

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCIN 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			47	2	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	1

Variants in CCIN

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

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

Position	Type	Phenotype	Significance	ClinVar
9-36169519-C-T		not specified	Uncertain significance (Jan 26, 2022)
9-36169614-G-A		not specified	Uncertain significance (Nov 06, 2023)
9-36169627-A-T		Spermatogenic failure 91	Pathogenic (May 24, 2024)
9-36169653-C-T		not specified	Uncertain significance (Jun 23, 2023)
9-36169668-C-T		not specified	Uncertain significance (Nov 03, 2022)
9-36169695-G-A		not specified	Likely benign (Nov 24, 2024)
9-36169732-T-C		Spermatogenic failure 91	Pathogenic (May 24, 2024)
9-36169819-G-T		not specified	Uncertain significance (Mar 03, 2025)
9-36169843-C-G		not specified	Uncertain significance (Aug 20, 2024)
9-36169890-C-T		not specified	Uncertain significance (Dec 13, 2021)
9-36169906-G-A		not specified	Uncertain significance (Jun 21, 2022)
9-36169908-T-C		not specified	Uncertain significance (Nov 23, 2022)
9-36169953-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-36169972-G-A		not specified	Uncertain significance (Sep 25, 2024)
9-36170031-C-T		not specified	Uncertain significance (Apr 12, 2022)
9-36170055-C-T		not specified	Uncertain significance (Sep 26, 2023)
9-36170056-G-A		not specified	Uncertain significance (Feb 12, 2024)
9-36170092-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-36170100-G-A		not specified	Uncertain significance (Jan 29, 2024)
9-36170101-C-A		not specified	Uncertain significance (Mar 29, 2023)
9-36170110-A-G		not specified	Uncertain significance (Feb 27, 2024)
9-36170125-G-T		not specified	Uncertain significance (Apr 22, 2022)
9-36170136-C-T		not specified	Uncertain significance (May 24, 2024)
9-36170149-T-C		not specified	Uncertain significance (Aug 12, 2024)
9-36170164-A-G		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCIN	protein_coding	protein_coding	ENST00000335119	1	1941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.124	0.871	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	286	355	0.806	0.0000218	3883
Missense in Polyphen		68	109.61	0.62039		1234
Synonymous	-0.738	153	142	1.08	0.00000842	1189
Loss of Function	2.47	4	14.0	0.286	6.62e-7	185

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

• Function: FUNCTION: Possible morphogenetic cytoskeletal element in spermiogenic differentiation.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.435
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.52

Haploinsufficiency Scores

• pHI: 0.548
• hipred: N
• hipred_score: 0.297
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccin

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: nucleus;cytoskeletal calyx