CYLC2

cylicin 2

Basic information

Region (hg38): 9:102995311-103018488

Links

ENSG00000155833 ∙ NCBI:1539 ∙ OMIM:604035 ∙ HGNC:2583 ∙ Uniprot:Q14093 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYLC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYLC2 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	5		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	5	0

Variants in CYLC2

This is a list of pathogenic ClinVar variants found in the CYLC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-103003183-G-T		not specified	Likely benign (Apr 12, 2022)
9-103003201-C-T		not specified	Uncertain significance (Jul 26, 2021)
9-103003208-G-A		not specified	Uncertain significance (Dec 06, 2021)
9-103004725-C-G		not specified	Uncertain significance (Dec 27, 2022)
9-103004726-G-A		not specified	Likely benign (Jan 03, 2022)
9-103004734-C-T		not specified	Uncertain significance (Apr 08, 2024)
9-103004735-C-A		not specified	Uncertain significance (Aug 12, 2021)
9-103004798-G-C		not specified	Uncertain significance (Jan 26, 2022)
9-103004972-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-103005099-T-A		not specified	Uncertain significance (Dec 05, 2022)
9-103005155-C-T		not specified	Uncertain significance (Jul 28, 2021)
9-103005232-G-C		not specified	Uncertain significance (Jan 03, 2022)
9-103005236-C-T		not specified	Uncertain significance (Dec 28, 2023)
9-103005296-A-G		not specified	Uncertain significance (Aug 04, 2021)
9-103005350-A-C		not specified	Uncertain significance (Jun 28, 2023)
9-103005359-A-G		not specified	Uncertain significance (Jun 11, 2024)
9-103005363-T-A		not specified	Uncertain significance (Feb 14, 2024)
9-103005374-A-T		not specified	Uncertain significance (May 06, 2024)
9-103005385-A-C		not specified	Uncertain significance (Oct 10, 2023)
9-103005401-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-103005491-A-G		not specified	Uncertain significance (Sep 28, 2022)
9-103005517-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-103005536-A-C		not specified	Uncertain significance (Aug 09, 2021)
9-103005539-T-A		not specified	Likely benign (Sep 22, 2023)
9-103005553-A-G		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYLC2	protein_coding	protein_coding	ENST00000374798	5	23178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000448	0.410	125670	0	39	125709	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.42	223	171	1.30	0.00000874	2293
Missense in Polyphen		35	34.963	1.0011		416
Synonymous	-1.21	72	60.1	1.20	0.00000300	584
Loss of Function	0.479	9	10.7	0.842	4.47e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000790	0.000787
Ashkenazi Jewish	0.000103	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000811	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000148	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0772

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 1.78
• rvis_percentile_EVS: 96.83

Haploinsufficiency Scores

• pHI: 0.0839
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0391

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cylc2

Gene ontology

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