CCNL2

cyclin L2, the group of Cyclins

Basic information

Region (hg38): 1:1385711-1399335

Previous symbols: [ "CCNM" ]

Links

ENSG00000221978 ∙ NCBI:81669 ∙ OMIM:613482 ∙ HGNC:20570 ∙ Uniprot:Q96S94 ∙ 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 CCNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNL2 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			40	2		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	1	2
Total	0	0	40	7	1

Variants in CCNL2

This is a list of pathogenic ClinVar variants found in the CCNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1387227-C-T		CCNL2-related disorder	Benign (Sep 25, 2019)
1-1387277-C-T		not specified	Likely benign (Oct 12, 2021)
1-1387286-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-1387305-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-1387332-G-T		not specified	Uncertain significance (Jan 22, 2024)
1-1387373-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-1387374-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-1387385-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-1387406-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-1387455-G-A		not specified	Uncertain significance (Jan 19, 2022)
1-1387488-C-T		not specified	Uncertain significance (May 09, 2023)
1-1387497-G-C		not specified	Uncertain significance (May 20, 2024)
1-1387780-C-A		not specified	Uncertain significance (Jan 16, 2024)
1-1387792-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-1387846-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-1387858-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-1387961-C-T		not specified	Uncertain significance (Dec 05, 2022)
1-1387975-T-C		not specified	Uncertain significance (Jun 28, 2023)
1-1387987-G-C		not specified	Uncertain significance (May 30, 2024)
1-1387996-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-1388033-G-T		not specified	Uncertain significance (Mar 29, 2023)
1-1390238-G-C		not specified	Uncertain significance (Nov 06, 2023)
1-1390246-A-G		CCNL2-related disorder	Likely benign (Aug 28, 2019)
1-1390255-C-T		CCNL2-related disorder	Likely benign (Feb 20, 2019)
1-1390277-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNL2	protein_coding	protein_coding	ENST00000400809	11	13618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.161	0.839	112711	449	12588	125748	0.0533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.538	312	340	0.918	0.0000222	3315
Missense in Polyphen		100	141.71	0.70568		1486
Synonymous	-1.20	152	134	1.13	0.00000799	1084
Loss of Function	3.68	7	28.0	0.250	0.00000177	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.107	0.107
Ashkenazi Jewish	0.0265	0.0265
East Asian	0.0838	0.0840
Finnish	0.103	0.102
European (Non-Finnish)	0.0399	0.0399
Middle Eastern	0.0838	0.0840
South Asian	0.0785	0.0785
Other	0.0582	0.0580

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing. May induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. {ECO:0000269|PubMed:14684736, ECO:0000269|PubMed:18216018}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.634
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.666
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnl2

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;nuclear speck;intracellular membrane-bounded organelle
• Molecular function: protein binding;cyclin-dependent protein serine/threonine kinase regulator activity