CRP

C-reactive protein, the group of Short pentraxins

Basic information

Region (hg38): 1:159712288-159714589

Links

ENSG00000132693 ∙ NCBI:1401 ∙ OMIM:123260 ∙ HGNC:2367 ∙ Uniprot:P02741 ∙ 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 CRP gene.

• Inborn genetic diseases (6 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRP 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	4
missense			5	1		6
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	5	4	2

Variants in CRP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-159712443-C-T		Inflammation	Uncertain significance (-)
1-159713554-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-159713564-C-A			Likely benign (Jun 13, 2018)
1-159713565-A-G		not specified	Likely benign (Dec 20, 2021)
1-159713581-C-G		not specified	Uncertain significance (Apr 27, 2022)
1-159713624-G-C		not specified	Uncertain significance (Mar 27, 2023)
1-159713679-A-G		CRP-related disorder	Uncertain significance (Nov 22, 2023)
1-159713704-C-T		not specified	Uncertain significance (Jul 14, 2022)
1-159713840-G-A			Likely benign (Aug 22, 2018)
1-159713843-C-G		CRP-related disorder	Uncertain significance (Feb 01, 2024)
1-159713861-G-A			Likely benign (Jun 01, 2022)
1-159713898-A-G		not specified	Uncertain significance (Aug 16, 2022)
1-159713988-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-159713988-G-C		not specified	Uncertain significance (Jul 12, 2022)
1-159714024-G-A		CRP-related disorder	Likely benign (Mar 27, 2023)
1-159714051-G-C		not specified	Uncertain significance (Dec 17, 2023)
1-159714071-C-T			Benign (Jul 11, 2018)
1-159714095-A-C			Benign (Jul 07, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRP	protein_coding	protein_coding	ENST00000255030	2	2301

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00370	0.416	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.252	129	121	1.06	0.00000663	1462
Missense in Polyphen		36	44.095	0.81643		592
Synonymous	-0.966	61	52.1	1.17	0.00000328	444
Loss of Function	-0.538	3	2.15	1.40	9.22e-8	24

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000553	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays several functions associated with host defense: it promotes agglutination, bacterial capsular swelling, phagocytosis and complement fixation through its calcium-dependent binding to phosphorylcholine. Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells.
• Pathway: Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Human Complement System;Overview of nanoparticle effects;IL-6 signaling pathway;Innate Immune System;Immune System;Initial triggering of complement;Classical antibody-mediated complement activation;Creation of C4 and C2 activators;Complement cascade;Leptin;IL6-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.443

Intolerance Scores

• loftool: 0.712
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0484
• hipred: N
• hipred_score: 0.180
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.395

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crp
• Phenotype: homeostasis/metabolism phenotype; immune system 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)

Gene ontology

• Biological process: acute-phase response;inflammatory response;complement activation, classical pathway;opsonization;positive regulation of gene expression;negative regulation of macrophage derived foam cell differentiation;negative regulation of lipid storage;positive regulation of superoxide anion generation;innate immune response;defense response to Gram-positive bacterium;negative regulation of blood vessel diameter;regulation of interleukin-8 secretion
• Cellular component: extracellular region;extracellular space
• Molecular function: complement component C1q binding;calcium ion binding;protein binding;low-density lipoprotein particle binding;choline binding;identical protein binding;virion binding;low-density lipoprotein particle receptor binding