CRTC3

CREB regulated transcription coactivator 3

Basic information

Region (hg38): 15:90529922-90645345

Links

ENSG00000140577 ∙ NCBI:64784 ∙ OMIM:608986 ∙ HGNC:26148 ∙ Uniprot:Q6UUV7 ∙ 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 CRTC3 gene.

• Inborn genetic diseases (20 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRTC3 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	2	3
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	2

Variants in CRTC3

This is a list of pathogenic ClinVar variants found in the CRTC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-90530122-G-C		not specified	Uncertain significance (Oct 17, 2023)
15-90530197-G-A			Likely benign (Mar 01, 2023)
15-90540072-A-C		not specified	Uncertain significance (May 26, 2023)
15-90602327-G-A		not specified	Uncertain significance (Jul 09, 2021)
15-90602349-A-G		not specified	Uncertain significance (Dec 03, 2021)
15-90604429-T-C		not specified	Uncertain significance (May 01, 2023)
15-90604438-C-T		not specified	Uncertain significance (Oct 13, 2023)
15-90607453-G-C		not specified	Uncertain significance (Jan 17, 2023)
15-90617932-G-A			Benign (Feb 07, 2018)
15-90625805-G-A		not specified	Uncertain significance (Oct 03, 2023)
15-90625991-C-T		not specified	Uncertain significance (Jan 26, 2023)
15-90629273-C-T		not specified	Uncertain significance (Jul 12, 2022)
15-90629324-C-T		not specified	Uncertain significance (Apr 27, 2022)
15-90629434-G-A		not specified	Uncertain significance (Nov 03, 2023)
15-90629447-C-T		not specified	Uncertain significance (Aug 17, 2022)
15-90629519-A-G		not specified	Uncertain significance (Oct 27, 2022)
15-90638446-A-G		not specified	Uncertain significance (Mar 01, 2023)
15-90638489-A-C		not specified	Uncertain significance (Oct 29, 2021)
15-90638566-C-A		Malignant tumor of prostate	Uncertain significance (-)
15-90638603-C-G		not specified	Uncertain significance (Mar 02, 2023)
15-90638606-C-T		not specified	Uncertain significance (Feb 27, 2024)
15-90638618-A-T		not specified	Uncertain significance (Feb 23, 2023)
15-90638639-C-T		not specified	Uncertain significance (Jun 02, 2023)
15-90638752-C-G		not specified	Uncertain significance (Nov 07, 2023)
15-90638768-G-C		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRTC3	protein_coding	protein_coding	ENST00000268184	15	115421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.866	0.134	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.401	327	348	0.940	0.0000199	3984
Missense in Polyphen		91	111.85	0.81359		1237
Synonymous	-2.44	182	145	1.26	0.00000833	1305
Loss of Function	4.35	6	33.0	0.182	0.00000182	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
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 the expression of specific CREB-activated 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:15454081, ECO:0000269|PubMed:15466468, ECO:0000269|PubMed:16817901, ECO:0000269|PubMed:16980408, ECO:0000269|PubMed:17210223, ECO:0000269|PubMed:17644518}.
• Pathway: HTLV-I infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.399
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.518
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.802

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crtc3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); liver/biliary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: viral process;positive regulation of CREB transcription factor activity;macrophage activation;negative regulation of cAMP-mediated signaling;positive regulation of transcription by RNA polymerase II;negative regulation of lipid catabolic process;protein homotetramerization;energy homeostasis
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: cAMP response element binding protein binding