CREM

cAMP responsive element modulator, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 10:35126790-35212958

Links

ENSG00000095794 ∙ NCBI:1390 ∙ OMIM:123812 ∙ HGNC:2352 ∙ Uniprot:Q03060 ∙ 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 CREM gene.

• Inborn genetic diseases (7 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CREM 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					2	2
missense			7	1	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	3

Variants in CREM

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

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

Position	Type	Phenotype	Significance	ClinVar
10-35178983-A-T		not specified	Uncertain significance (Aug 13, 2021)
10-35179145-A-G		not specified	Uncertain significance (Dec 28, 2022)
10-35179179-G-A			Benign (Dec 31, 2019)
10-35179247-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-35179265-C-A		not specified	Uncertain significance (Jul 19, 2023)
10-35179265-C-T		not specified	Uncertain significance (Oct 22, 2021)
10-35188293-C-T		not specified	Uncertain significance (Mar 16, 2022)
10-35188305-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-35206928-G-A		not specified	Uncertain significance (Jun 02, 2023)
10-35206973-C-T			Likely benign (Mar 29, 2018)
10-35207028-A-G			Benign (Jun 29, 2018)
10-35211742-A-G		not specified	Uncertain significance (Feb 06, 2023)
10-35211745-A-G			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CREM	protein_coding	protein_coding	ENST00000345491	7	86168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.509	0.491	125710	0	18	125728	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	145	162	0.898	0.00000801	1922
Missense in Polyphen		41	58.474	0.70117		679
Synonymous	-0.0895	55	54.2	1.02	0.00000268	611
Loss of Function	3.23	4	19.3	0.207	0.00000124	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000555	0.0000527
Middle Eastern	0.0000546	0.0000544
South Asian	0.000269	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that binds the cAMP response element (CRE), a sequence present in many viral and cellular promoters. Isoforms are either transcriptional activators or repressors. Plays a role in spermatogenesis and is involved in spermatid maturation (PubMed:10373550). {ECO:0000269|PubMed:10373550}.
• Pathway: HTLV-I infection - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;repression of pain sensation by the transcriptional regulator dream;regulation of spermatogenesis by crem;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Calcium signaling in the CD4+ TCR pathway (Consensus)

Recessive Scores

• pRec: 0.256

Intolerance Scores

• loftool: 0.760
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.800
• hipred: Y
• hipred_score: 0.825

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crem
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; muscle 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;glucose metabolic process;regulation of transcription, DNA-templated;fatty acid metabolic process;glycosphingolipid metabolic process;signal transduction;multicellular organism development;spermatogenesis;cell differentiation;regulation of circadian rhythm;positive regulation of transcription by RNA polymerase II;retinoic acid receptor signaling pathway;rhythmic process
• Cellular component: nucleus;transcription factor complex;cytoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;protein binding;cAMP response element binding protein binding