CIRBP

cold inducible RNA binding protein, the group of RNA binding motif containing

Basic information

Region (hg38): 19:1259384-1274880

Links

ENSG00000099622 ∙ NCBI:1153 ∙ OMIM:602649 ∙ HGNC:1982 ∙ Uniprot:Q14011 ∙ 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 CIRBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIRBP 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	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	0	2

Variants in CIRBP

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

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

Position	Type	Phenotype	Significance	ClinVar
19-1271130-C-T			Benign (Feb 26, 2018)
19-1271206-T-C		not specified	Uncertain significance (Aug 28, 2023)
19-1271390-G-A		not specified	Uncertain significance (Dec 16, 2023)
19-1271429-T-A		not specified	Uncertain significance (Jun 28, 2022)
19-1271452-C-T		not specified	Uncertain significance (Oct 09, 2024)
19-1271453-G-T		not specified	Uncertain significance (Dec 14, 2023)
19-1271462-C-G		not specified	Uncertain significance (Apr 11, 2023)
19-1271465-G-A		not specified	Uncertain significance (Jan 20, 2023)
19-1271569-A-G		not specified	Uncertain significance (Nov 27, 2024)
19-1271598-G-C		not specified	Uncertain significance (Aug 13, 2021)
19-1272018-G-A		not specified	Uncertain significance (Apr 12, 2023)
19-1272021-G-A		not specified	Uncertain significance (Nov 13, 2024)
19-1272188-C-G			Benign (Feb 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIRBP	protein_coding	protein_coding	ENST00000588030	6	15496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.336	0.661	125592	0	4	125596	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.839	90	115	0.780	0.00000785	1105
Missense in Polyphen		5	26.24	0.19055		313
Synonymous	-1.32	54	43.0	1.26	0.00000284	338
Loss of Function	2.57	3	13.0	0.231	8.96e-7	115

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)	0.0000374	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold- induced suppression of cell proliferation. Binds specifically to the 3'-untranslated regions (3'-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor (By similarity). Promotes assembly of stress granules (SGs), when overexpressed. {ECO:0000250, ECO:0000269|PubMed:11574538, ECO:0000269|PubMed:16513844}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.378
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.138
• hipred: Y
• hipred_score: 0.833
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cirbp
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: response to cold;response to UV;negative regulation of translation;stress granule assembly;positive regulation of translation;positive regulation of mRNA splicing, via spliceosome;mRNA stabilization
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;nucleolus;cytoplasm;cytoplasmic stress granule;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;poly(U) RNA binding;translation repressor activity;small ribosomal subunit rRNA binding