CREG2

cellular repressor of E1A stimulated genes 2

Basic information

Region (hg38): 2:101345550-101387503

Links

ENSG00000175874 ∙ NCBI:200407 ∙ OMIM:618540 ∙ HGNC:14272 ∙ Uniprot:Q8IUH2 ∙ 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 CREG2 gene.

• not_specified (46 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CREG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153836.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			46			46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CREG2	protein_coding	protein_coding	ENST00000324768	4	42045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000730	0.523	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	96	113	0.846	0.00000582	1847
Missense in Polyphen		38	45.061	0.8433		677
Synonymous	0.590	39	44.0	0.887	0.00000243	591
Loss of Function	0.528	7	8.68	0.807	4.56e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000409	0.000409
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Vitamin D Receptor Pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.221
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Creg2

Gene ontology

• Cellular component: extracellular region;endoplasmic reticulum;Golgi apparatus
• Molecular function: cofactor binding