CYTL1

cytokine like 1

Basic information

Region (hg38): 4:5014586-5019458

Links

ENSG00000170891 ∙ NCBI:54360 ∙ OMIM:607930 ∙ HGNC:24435 ∙ Uniprot:Q9NRR1 ∙ 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 CYTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTL1 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in CYTL1

This is a list of pathogenic ClinVar variants found in the CYTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-5015155-C-T		not specified	Uncertain significance (May 25, 2022)
4-5015161-C-T		not specified	Likely benign (Aug 10, 2023)
4-5015162-G-C		not specified	Uncertain significance (Nov 09, 2022)
4-5015167-G-C		not specified	Uncertain significance (Jun 02, 2023)
4-5015176-G-A		not specified	Uncertain significance (Dec 16, 2023)
4-5015231-A-C		not specified	Uncertain significance (Jan 27, 2022)
4-5016884-C-G		not specified	Uncertain significance (Apr 09, 2024)
4-5016898-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-5016918-G-A		not specified	Uncertain significance (Sep 27, 2021)
4-5016933-A-G		not specified	Uncertain significance (Nov 23, 2022)
4-5019301-C-G		not specified	Uncertain significance (Oct 04, 2022)
4-5019304-A-G		not specified	Uncertain significance (Mar 15, 2024)
4-5019393-G-C		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTL1	protein_coding	protein_coding	ENST00000307746	4	4887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000107	0.208	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	69	71.7	0.962	0.00000405	842
Missense in Polyphen		23	23.345	0.98523		305
Synonymous	0.537	29	32.9	0.881	0.00000176	293
Loss of Function	-0.371	7	6.02	1.16	3.53e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.333
• hipred: N
• hipred_score: 0.198

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cytl1
• Phenotype: skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: chondrocyte differentiation;signal transduction;positive regulation of transcription by RNA polymerase II;inner ear development;chondroitin sulfate proteoglycan biosynthetic process;positive regulation of DNA-binding transcription factor activity;cartilage homeostasis
• Cellular component: extracellular space
• Molecular function: signaling receptor binding