CYLC1

cylicin 1

Basic information

Region (hg38): X:83861126-83886699

Links

ENSG00000183035 ∙ NCBI:1538 ∙ OMIM:300768 ∙ HGNC:2582 ∙ Uniprot:P35663 ∙ 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, X-linked, 8	XL	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	38013430; 38573307

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYLC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYLC1 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				4		4
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	41	6	0

Variants in CYLC1

This is a list of pathogenic ClinVar variants found in the CYLC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-83861203-A-G			Likely benign (Feb 01, 2024)
X-83871489-C-T			Likely benign (Sep 01, 2022)
X-83871517-C-A		not specified	Conflicting classifications of pathogenicity (Mar 15, 2024)
X-83872889-C-T		not specified	Uncertain significance (Jan 10, 2022)
X-83872907-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-83872908-A-G		not specified	Uncertain significance (Jan 26, 2025)
X-83872939-A-G		not specified	Uncertain significance (Dec 03, 2021)
X-83872982-A-G		not specified	Uncertain significance (Oct 20, 2024)
X-83873061-C-T		not specified	Uncertain significance (Sep 24, 2024)
X-83873095-A-C		not specified	Uncertain significance (Jun 22, 2024)
X-83873115-G-A		not specified	Uncertain significance (Nov 20, 2024)
X-83873132-C-T		not specified	Uncertain significance (Mar 20, 2023)
X-83873149-A-C			Likely benign (Aug 01, 2022)
X-83873151-T-C		not specified	Uncertain significance (Mar 06, 2023)
X-83873171-C-G		not specified	Uncertain significance (Aug 30, 2021)
X-83873192-C-T		not specified	Uncertain significance (Jul 14, 2021)
X-83873283-C-T		not specified	Uncertain significance (Feb 18, 2025)
X-83873289-A-G		not specified	Uncertain significance (Nov 19, 2022)
X-83873294-T-A		not specified	Uncertain significance (Aug 28, 2024)
X-83873405-C-T			Likely benign (Mar 01, 2023)
X-83873406-C-T		not specified	Uncertain significance (Feb 08, 2025)
X-83873527-A-T			Likely benign (Dec 01, 2023)
X-83873528-A-G		not specified	Uncertain significance (Jun 05, 2024)
X-83873530-G-T		not specified	Uncertain significance (Jun 03, 2022)
X-83873538-C-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYLC1	protein_coding	protein_coding	ENST00000329312	5	25552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.931	0.0685	115979	0	1	115980	0.00000431

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.53	241	183	1.32	0.0000120	4278
Missense in Polyphen		49	32.006	1.531		801
Synonymous	-1.63	84	67.1	1.25	0.00000445	1132
Loss of Function	3.08	1	12.9	0.0773	8.20e-7	416

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)	0.0000128	0.00000943
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible architectural role during spermatogenesis. May be involved in spermatid differentiation.

Recessive Scores

• pRec: 0.0626

Intolerance Scores

• loftool: 0.120
• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cylc1

Gene ontology

• Biological process: cytoskeleton organization;multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: nucleus;cytoskeletal calyx;acrosomal matrix
• Molecular function: structural molecule activity;structural constituent of cytoskeleton