CREG1

cellular repressor of E1A stimulated genes 1

Basic information

Region (hg38): 1:167529117-167553805

Previous symbols: [ "CREG" ]

Links

ENSG00000143162 ∙ NCBI:8804 ∙ OMIM:618055 ∙ HGNC:2351 ∙ Uniprot:O75629 ∙ 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 CREG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CREG1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in CREG1

This is a list of pathogenic ClinVar variants found in the CREG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167546113-T-A		not specified	Uncertain significance (Mar 07, 2024)
1-167546138-T-A		not specified	Uncertain significance (Dec 27, 2023)
1-167546149-C-T		not specified	Uncertain significance (May 08, 2023)
1-167546184-C-A		not specified	Uncertain significance (Jun 19, 2024)
1-167546239-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-167548088-C-A		not specified	Uncertain significance (Mar 31, 2024)
1-167553485-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-167553486-C-G		not specified	Uncertain significance (Apr 08, 2024)
1-167553487-G-A		CREG1-related disorder	Likely benign (Jul 12, 2019)
1-167553501-G-T		not specified	Uncertain significance (Oct 05, 2023)
1-167553602-G-A		not specified	Uncertain significance (Mar 28, 2022)
1-167553610-G-A		CREG1-related disorder	Likely benign (Apr 12, 2019)
1-167553611-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-167553631-G-T		not specified	Uncertain significance (Feb 27, 2024)
1-167553653-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-167553665-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-167553699-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-167553710-G-A		not specified	Uncertain significance (Dec 02, 2022)
1-167553726-G-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CREG1	protein_coding	protein_coding	ENST00000370509	4	24091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00122	0.652	125724	0	11	125735	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	67	77.5	0.865	0.00000366	1383
Missense in Polyphen		37	35.654	1.0377		540
Synonymous	0.645	25	29.5	0.849	0.00000154	472
Loss of Function	0.643	5	6.81	0.734	3.52e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000133	0.000133
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000662	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May contribute to the transcriptional control of cell growth and differentiation. Antagonizes transcriptional activation and cellular transformation by the adenovirus E1A protein. The transcriptional control activity of cell growth requires interaction with IGF2R. {ECO:0000269|PubMed:12934103, ECO:0000269|PubMed:9710587}.
• Pathway: Senescence and Autophagy in Cancer;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.115

Haploinsufficiency Scores

• pHI: 0.583
• hipred: N
• hipred_score: 0.188
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.466

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Creg1
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;cell population proliferation;regulation of growth;neutrophil degranulation;negative regulation of nucleic acid-templated transcription
• Cellular component: extracellular region;extracellular space;transcription factor complex;azurophil granule lumen;extracellular exosome
• Molecular function: transcription corepressor activity;transcription factor binding;cofactor binding