MRC2

mannose receptor C type 2, the group of C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 17:62627670-62693597

Links

ENSG00000011028 ∙ NCBI:9902 ∙ OMIM:612264 ∙ HGNC:16875 ∙ Uniprot:Q9UBG0 ∙ 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 MRC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRC2 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						0
missense			73	1	2	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	73	1	2

Variants in MRC2

This is a list of pathogenic ClinVar variants found in the MRC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-62627866-C-T		not specified	Uncertain significance (Feb 23, 2023)
17-62664642-C-A		not specified	Uncertain significance (Jan 23, 2024)
17-62664770-G-A		not specified	Uncertain significance (Nov 30, 2022)
17-62664838-C-T		not specified	Uncertain significance (Jan 10, 2022)
17-62664839-G-A		not specified	Uncertain significance (Mar 25, 2022)
17-62664860-C-T		not specified	Uncertain significance (May 18, 2023)
17-62664892-A-G		not specified	Uncertain significance (Jul 09, 2021)
17-62664893-G-C			Benign (Feb 20, 2018)
17-62666126-A-G		not specified	Uncertain significance (Aug 16, 2021)
17-62666181-G-C		not specified	Uncertain significance (Apr 08, 2022)
17-62666204-C-G		not specified	Uncertain significance (Feb 16, 2023)
17-62666222-C-A		not specified	Uncertain significance (May 30, 2024)
17-62666231-G-A		not specified	Uncertain significance (Apr 25, 2023)
17-62666232-G-A		not specified	Uncertain significance (Mar 05, 2024)
17-62666244-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-62666526-A-G		not specified	Uncertain significance (Jun 18, 2024)
17-62666533-C-T		not specified	Uncertain significance (May 24, 2023)
17-62666568-G-C		not specified	Uncertain significance (Jun 02, 2024)
17-62666590-C-T		not specified	Uncertain significance (Aug 30, 2022)
17-62666869-T-G		not specified	Uncertain significance (Jun 21, 2022)
17-62671666-A-C		not specified	Uncertain significance (Jan 04, 2024)
17-62671732-C-T		not specified	Uncertain significance (Dec 09, 2023)
17-62671816-A-C		not specified	Uncertain significance (Oct 17, 2023)
17-62672151-C-T		not specified	Uncertain significance (Jan 27, 2022)
17-62674110-C-G		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRC2	protein_coding	protein_coding	ENST00000303375	30	66197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.675	0.325	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	661	890	0.743	0.0000578	9603
Missense in Polyphen		179	322.98	0.55421		3614
Synonymous	1.23	343	373	0.919	0.0000262	2798
Loss of Function	6.77	19	87.3	0.218	0.00000427	876

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000491	0.000490
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000379	0.000370
European (Non-Finnish)	0.000128	0.000114
Middle Eastern	0.000111	0.000109
South Asian	0.000200	0.000196
Other	0.000499	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. Internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. May be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. May contribute to cellular uptake, remodeling and degradation of extracellular collagen matrices. May play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. May participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). {ECO:0000269|PubMed:10683150, ECO:0000269|PubMed:12972549}.
• Pathway: Phagosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Immune System;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Cross-presentation of soluble exogenous antigens (endosomes) (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.532
• rvis_EVS: -1.16
• rvis_percentile_EVS: 6.09

Haploinsufficiency Scores

• pHI: 0.683
• hipred: Y
• hipred_score: 0.693
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.509

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrc2
• Phenotype: cellular phenotype; immune system phenotype; normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: osteoblast differentiation;endocytosis;collagen catabolic process
• Cellular component: focal adhesion;membrane;integral component of membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;collagen binding;carbohydrate binding