CRY2

cryptochrome circadian regulator 2

Basic information

Region (hg38): 11:45847117-45883248

Links

ENSG00000121671 ∙ NCBI:1408 ∙ OMIM:603732 ∙ HGNC:2385 ∙ Uniprot:Q49AN0 ∙ 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 CRY2 gene.

• Inborn genetic diseases (20 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRY2 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					1	1
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	2

Variants in CRY2

This is a list of pathogenic ClinVar variants found in the CRY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-45847449-T-C		not specified	Uncertain significance (Jan 17, 2023)
11-45847462-C-A			Benign (Jul 16, 2018)
11-45847501-C-G		not specified	Uncertain significance (Jun 21, 2022)
11-45847531-C-A		not specified	Uncertain significance (Jan 23, 2024)
11-45847531-C-T		not specified	Uncertain significance (Feb 10, 2023)
11-45847550-C-G		not specified	Uncertain significance (Dec 12, 2023)
11-45847651-A-G		not specified	Uncertain significance (Oct 05, 2021)
11-45858788-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-45858839-A-G		not specified	Uncertain significance (Aug 08, 2022)
11-45858840-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-45858861-A-G		not specified	Uncertain significance (Dec 03, 2021)
11-45860891-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-45860978-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-45862077-C-A		not specified	Uncertain significance (Feb 13, 2024)
11-45862140-G-A		not specified	Uncertain significance (Jun 03, 2022)
11-45867628-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-45867649-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-45867677-C-T			Benign (Jul 13, 2018)
11-45867726-T-C		not specified	Uncertain significance (May 26, 2022)
11-45867729-C-T		not specified	Uncertain significance (Sep 29, 2022)
11-45869578-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-45869618-C-T		not specified	Uncertain significance (Mar 28, 2023)
11-45869657-C-T		not specified	Uncertain significance (Jul 11, 2023)
11-45869675-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-45869749-G-C		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRY2	protein_coding	protein_coding	ENST00000443527	11	36130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000318	1.00	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	275	389	0.706	0.0000237	3972
Missense in Polyphen		51	114.72	0.44457		1181
Synonymous	-0.699	163	152	1.07	0.00000865	1251
Loss of Function	3.38	12	32.9	0.364	0.00000183	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000458	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor which forms a core component of the circadian clock. The circadian clock, an internal time- keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK|NPAS2-ARNTL/BMAL1|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. CRY1 and CRY2 have redundant functions but also differential and selective contributions at least in defining the pace of the SCN circadian clock and its circadian transcriptional outputs. Less potent transcriptional repressor in cerebellum and liver than CRY1, though less effective in lengthening the period of the SCN oscillator. Seems to play a critical role in tuning SCN circadian period by opposing the action of CRY1. With CRY1, dispensable for circadian rhythm generation but necessary for the development of intercellular networks for rhythm synchrony. May mediate circadian regulation of cAMP signaling and gluconeogenesis by blocking glucagon-mediated increases in intracellular cAMP concentrations and in CREB1 phosphorylation. Besides its role in the maintenance of the circadian clock, is also involved in the regulation of other processes. Plays a key role in glucose and lipid metabolism modulation, in part, through the transcriptional regulation of genes involved in these pathways, such as LEP or ACSL4. Represses glucocorticoid receptor NR3C1/GR-induced transcriptional activity by binding to glucocorticoid response elements (GREs). Represses the CLOCK-ARNTL/BMAL1 induced transcription of BHLHE40/DEC1. Represses the CLOCK-ARNTL/BMAL1 induced transcription of NAMPT (By similarity). {ECO:0000250|UniProtKB:Q9R194, ECO:0000269|PubMed:10531061, ECO:0000269|PubMed:14672706, ECO:0000269|PubMed:16790549}.
• Pathway: Circadian rhythm - Homo sapiens (human);Circadian Clock;Melatonin metabolism and effects;BMAL1-CLOCK,NPAS2 activates circadian gene expression;Exercise-induced Circadian Regulation;Circadian Clock;Circadian rhythm pathway (Consensus)

Recessive Scores

• pRec: 0.187

Intolerance Scores

• loftool: 0.0484
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.395
• hipred: Y
• hipred_score: 0.748
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cry2
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;photoreactive repair;circadian rhythm;response to light stimulus;blue light signaling pathway;protein-chromophore linkage;negative regulation of phosphoprotein phosphatase activity;circadian regulation of gene expression;glucose homeostasis;regulation of circadian rhythm;negative regulation of circadian rhythm;entrainment of circadian clock by photoperiod;negative regulation of transcription, DNA-templated;regulation of sodium-dependent phosphate transport;negative regulation of glucocorticoid receptor signaling pathway
• Cellular component: extracellular region;nucleus;cytosol;nuclear speck
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA binding;damaged DNA binding;single-stranded DNA binding;deoxyribodipyrimidine photo-lyase activity;DNA (6-4) photolyase activity;protein binding;blue light photoreceptor activity;phosphatase binding;FAD binding