CREBRF

CREB3 regulatory factor

Basic information

Region (hg38): 5:173056352-173139284

Previous symbols: [ "C5orf41" ]

Links

ENSG00000164463 ∙ NCBI:153222 ∙ OMIM:617109 ∙ HGNC:24050 ∙ Uniprot:Q8IUR6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inherited obesity (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CREBRF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CREBRF 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	1	2

Variants in CREBRF

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

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

Position	Type	Phenotype	Significance	ClinVar
5-173086559-C-T		not specified	Uncertain significance (Dec 21, 2024)
5-173090405-G-A		not specified	Uncertain significance (Aug 21, 2024)
5-173090418-A-G		not specified	Uncertain significance (Feb 08, 2025)
5-173090639-C-T		not specified	Uncertain significance (Dec 30, 2023)
5-173090650-C-T			Benign (Aug 02, 2017)
5-173090678-C-A		not specified	Uncertain significance (Oct 12, 2022)
5-173090679-C-T		not specified	Uncertain significance (Dec 13, 2022)
5-173090739-C-G		not specified	Uncertain significance (Apr 14, 2022)
5-173090804-T-G		not specified	Uncertain significance (Feb 14, 2025)
5-173090838-A-T		not specified	Uncertain significance (Nov 22, 2023)
5-173090857-C-A		not specified	Uncertain significance (Mar 31, 2024)
5-173090862-A-G		not specified	Uncertain significance (Dec 07, 2024)
5-173090905-C-G		not specified	Uncertain significance (Jan 10, 2025)
5-173090907-A-G		not specified	Uncertain significance (Oct 01, 2024)
5-173090910-C-T		not specified	Uncertain significance (Nov 27, 2023)
5-173090924-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-173090941-G-C		not specified	Uncertain significance (Sep 22, 2022)
5-173090945-C-G		not specified	Uncertain significance (Dec 14, 2024)
5-173090975-T-A		not specified	Uncertain significance (Nov 28, 2024)
5-173090976-A-G		not specified	Uncertain significance (Nov 13, 2024)
5-173090985-C-A		not specified	Uncertain significance (Mar 16, 2022)
5-173091029-G-C		not specified	Uncertain significance (Oct 23, 2024)
5-173091051-C-T		not specified	Uncertain significance (Feb 20, 2025)
5-173091073-A-G			Likely benign (Jan 01, 2024)
5-173091109-A-G			Benign (Aug 02, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CREBRF	protein_coding	protein_coding	ENST00000296953	8	82937

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000254	125399	0	2	125401	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	211	332	0.635	0.0000163	4223
Missense in Polyphen		58	140.19	0.41371		1744
Synonymous	1.71	98	122	0.804	0.00000609	1166
Loss of Function	5.06	0	29.8	0.00	0.00000150	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of the endoplasmic reticulum stress response or unfolded protein response (UPR). Represses the transcriptional activity of CREB3 during the UPR. Recruits CREB3 into nuclear foci. {ECO:0000269|PubMed:18391022}.
• Pathway: Unfolded Protein Response (UPR);Metabolism of proteins;CREB3 factors activate genes (Consensus)

Recessive Scores

• pRec: 0.0744

Intolerance Scores

• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.407
• hipred: Y
• hipred_score: 0.739
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crebrf
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: endoplasmic reticulum unfolded protein response;maternal behavior;positive regulation of transcription by RNA polymerase II;negative regulation of glucocorticoid mediated signaling pathway;positive regulation of prolactin signaling pathway
• Cellular component: nucleus;nucleoplasm;nuclear body
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding