CLEC4M

C-type lectin domain family 4 member M, the group of CD molecules

Basic information

Region (hg38): 19:7763210-7769605

Previous symbols: [ "CD209L", "CD299" ]

Links

ENSG00000104938 ∙ NCBI:10332 ∙ OMIM:605872 ∙ HGNC:13523 ∙ Uniprot:Q9H2X3 ∙ 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 CLEC4M gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC4M 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			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	5	0

Variants in CLEC4M

This is a list of pathogenic ClinVar variants found in the CLEC4M region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7763395-G-A		not specified	Uncertain significance (Apr 26, 2023)
19-7765658-C-A		not specified	Uncertain significance (Jun 18, 2021)
19-7765763-C-A		not specified	Uncertain significance (May 28, 2023)
19-7765789-A-G		not specified	Likely benign (Jun 01, 2023)
19-7765790-G-T		not specified	Uncertain significance (Nov 29, 2023)
19-7765791-T-C		not specified	Uncertain significance (Jun 06, 2023)
19-7765826-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-7765845-G-A		not specified	Likely benign (Jun 11, 2021)
19-7765857-C-T		not specified	Uncertain significance (May 23, 2024)
19-7765871-C-A		not specified	Uncertain significance (Jul 06, 2024)
19-7765952-A-G		not specified	Uncertain significance (Dec 17, 2023)
19-7766050-G-A			Likely benign (Jan 01, 2023)
19-7766121-A-G			Likely benign (Feb 01, 2023)
19-7766132-G-A		not specified	Uncertain significance (Mar 03, 2022)
19-7766157-C-T		not specified	Uncertain significance (Nov 29, 2023)
19-7766680-A-G		not specified	Uncertain significance (Feb 13, 2024)
19-7766684-C-A		not specified	Likely benign (Feb 13, 2024)
19-7766782-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-7766787-A-G		not specified	Uncertain significance (May 31, 2023)
19-7767594-T-C		not specified	Uncertain significance (Jun 10, 2024)
19-7768840-T-C		not specified	Uncertain significance (Mar 01, 2024)
19-7768966-C-T		not specified	Uncertain significance (Mar 12, 2024)
19-7768969-C-G		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC4M	protein_coding	protein_coding	ENST00000327325	7	6457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.56e-7	0.708	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.916	166	203	0.819	0.0000114	2586
Missense in Polyphen		91	111.11	0.81903		1493
Synonymous	-0.0652	90	89.2	1.01	0.00000551	766
Loss of Function	1.18	12	17.3	0.693	7.51e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000163	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable pathogen-recognition receptor involved in peripheral immune surveillance in liver. May mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates. {ECO:0000269|PubMed:11257134}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Hepatitis C virus. {ECO:0000269|PubMed:15371595, ECO:0000269|PubMed:16816373}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Human coronavirus 229E. {ECO:0000269|PubMed:17037540}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Influenzavirus. {ECO:0000269|PubMed:21191006}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for West-nile virus. {ECO:0000269|PubMed:15479853}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Marburg virus glycoprotein. {ECO:0000269|PubMed:15479853}.
• Pathway: Phagosome - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Measles - Homo sapiens (human);Human Complement System;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host (Consensus)

Intolerance Scores

• loftool: 0.909
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.139
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.358

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response;endocytosis;leukocyte cell-cell adhesion;cell-cell recognition;modulation by virus of host morphology or physiology;virion attachment to host cell;viral genome replication;antigen processing and presentation;intracellular signal transduction;innate immune response;viral entry into host cell;peptide antigen transport;intracellular transport of virus
• Cellular component: extracellular region;cytoplasm;integral component of plasma membrane;membrane;host cell
• Molecular function: virus receptor activity;mannose binding;carbohydrate binding;ICAM-3 receptor activity;signaling receptor activity;peptide antigen binding;virion binding;metal ion binding;calcium-dependent protein binding