CRTC2

CREB regulated transcription coactivator 2

Basic information

Region (hg38): 1:153947669-153958615

Links

ENSG00000160741 ∙ NCBI:200186 ∙ OMIM:608972 ∙ HGNC:27301 ∙ Uniprot:Q53ET0 ∙ 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 CRTC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRTC2 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	0	0

Variants in CRTC2

This is a list of pathogenic ClinVar variants found in the CRTC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153948119-C-T		not specified	Uncertain significance (Feb 17, 2023)
1-153948129-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-153948164-G-C		not specified	Uncertain significance (Dec 16, 2023)
1-153948215-C-T		not specified	Uncertain significance (Jul 09, 2024)
1-153948220-C-G		not specified	Uncertain significance (Jun 09, 2022)
1-153948266-T-C		not specified	Uncertain significance (May 09, 2022)
1-153948282-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-153948308-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-153948481-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-153948493-G-C		not specified	Uncertain significance (May 21, 2024)
1-153948526-T-C		not specified	Uncertain significance (Aug 07, 2024)
1-153948609-G-C		not specified	Uncertain significance (Jan 10, 2023)
1-153949138-T-C		not specified	Uncertain significance (Dec 28, 2023)
1-153949163-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-153949180-G-A		not specified	Uncertain significance (Mar 07, 2023)
1-153949209-C-G		not specified	Uncertain significance (Oct 09, 2024)
1-153949294-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-153949315-T-C		not specified	Uncertain significance (Sep 12, 2024)
1-153949335-G-A		not specified	Uncertain significance (May 04, 2023)
1-153949381-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-153951289-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-153951364-G-T		not specified	Uncertain significance (Nov 29, 2023)
1-153951378-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-153951415-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-153951441-G-A		not specified	Uncertain significance (Oct 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRTC2	protein_coding	protein_coding	ENST00000368633	14	10957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00110	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.769	356	399	0.892	0.0000215	4412
Missense in Polyphen		143	179.59	0.79626		2033
Synonymous	-0.362	171	165	1.04	0.00000827	1538
Loss of Function	4.84	3	33.0	0.0909	0.00000205	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000562	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator for CREB1 which activates transcription through both consensus and variant cAMP response element (CRE) sites. Acts as a coactivator, in the SIK/TORC signaling pathway, being active when dephosphorylated and acts independently of CREB1 'Ser-133' phosphorylation. Enhances the interaction of CREB1 with TAF4. Regulates gluconeogenesis as a component of the LKB1/AMPK/TORC2 signaling pathway. Regulates the expression of specific genes such as the steroidogenic gene, StAR. Potent coactivator of PPARGC1A and inducer of mitochondrial biogenesis in muscle cells. Also coactivator for TAX activation of the human T-cell leukemia virus type 1 (HTLV-1) long terminal repeats (LTR). {ECO:0000269|PubMed:14506290, ECO:0000269|PubMed:14536081, ECO:0000269|PubMed:15454081, ECO:0000269|PubMed:16809310, ECO:0000269|PubMed:16817901, ECO:0000269|PubMed:16980408, ECO:0000269|PubMed:17210223}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Insulin resistance - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Metformin Pathway, Pharmacodynamic;AMP-activated Protein Kinase (AMPK) Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.237

Intolerance Scores

• loftool: 0.235
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.257
• hipred: Y
• hipred_score: 0.658
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crtc2
• Phenotype: liver/biliary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: gluconeogenesis;viral process;positive regulation of CREB transcription factor activity;glucose homeostasis;histone H3-K9 acetylation;positive regulation of transcription by RNA polymerase II;protein homotetramerization;toxin transport
• Cellular component: nucleus;nucleoplasm;cytoplasm;extracellular exosome
• Molecular function: chromatin binding;protein binding;cAMP response element binding protein binding