ASGR2

asialoglycoprotein receptor 2, the group of C-type lectin domain containing

Basic information

Region (hg38): 17:7101322-7115700

Links

ENSG00000161944 ∙ NCBI:433 ∙ OMIM:108361 ∙ HGNC:743 ∙ Uniprot:P07307 ∙ 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 ASGR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASGR2 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	2

Variants in ASGR2

This is a list of pathogenic ClinVar variants found in the ASGR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7101587-G-A			Benign (Apr 24, 2018)
17-7101590-G-A			Benign (Dec 31, 2019)
17-7101663-G-A		not specified	Uncertain significance (Jun 05, 2023)
17-7101685-C-G		not specified	Uncertain significance (Mar 28, 2024)
17-7101700-C-T		not specified	Uncertain significance (Jan 29, 2024)
17-7101706-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-7101729-A-C		not specified	Uncertain significance (Feb 27, 2023)
17-7102136-C-G		not specified	Uncertain significance (Jul 26, 2022)
17-7102145-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-7102165-T-C		not specified	Uncertain significance (Jan 31, 2024)
17-7102177-G-A		not specified	Uncertain significance (May 11, 2022)
17-7107119-C-T		not specified	Uncertain significance (Apr 04, 2023)
17-7107142-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-7107264-C-G		not specified	Likely benign (Apr 09, 2024)
17-7107270-G-A		not specified	Uncertain significance (Sep 25, 2023)
17-7107279-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-7107899-C-T		not specified	Uncertain significance (May 23, 2023)
17-7108477-C-G		not specified	Uncertain significance (Nov 09, 2023)
17-7108488-G-A		not specified	Likely benign (Jan 31, 2024)
17-7108500-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-7108534-G-A		not specified	Uncertain significance (Nov 17, 2022)
17-7108761-G-T		not specified	Uncertain significance (Sep 14, 2023)
17-7108822-A-G		not specified	Uncertain significance (Aug 04, 2023)
17-7114132-T-C		not specified	Likely benign (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASGR2	protein_coding	protein_coding	ENST00000380952	8	14379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.81e-10	0.0905	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.285	176	187	0.941	0.0000109	2065
Missense in Polyphen		59	65.192	0.90502		810
Synonymous	0.228	75	77.5	0.967	0.00000500	571
Loss of Function	0.0601	14	14.2	0.983	6.09e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000323	0.000309
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000217	0.000217
South Asian	0.000171	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the endocytosis of plasma glycoproteins to which the terminal sialic acid residue on their complex carbohydrate moieties has been removed. The receptor recognizes terminal galactose and N-acetylgalactosamine units. After ligand binding to the receptor, the resulting complex is internalized and transported to a sorting organelle, where receptor and ligand are disassociated. The receptor then returns to the cell membrane surface.
• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation (Consensus)

Intolerance Scores

• loftool: 0.835
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.139
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asgr2
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;cell surface receptor signaling pathway;viral process;protein N-linked glycosylation via asparagine;bone mineralization;regulation of protein stability;lipid homeostasis
• Cellular component: plasma membrane;integral component of membrane;endoplasmic reticulum quality control compartment;perinuclear region of cytoplasm
• Molecular function: asialoglycoprotein receptor activity;protein binding;carbohydrate binding