CD180

CD180 molecule, the group of CD molecules

Basic information

Region (hg38): 5:67179613-67196799

Previous symbols: [ "LY64" ]

Links

ENSG00000134061 ∙ NCBI:4064 ∙ OMIM:602226 ∙ HGNC:6726 ∙ Uniprot:Q99467 ∙ 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 CD180 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD180 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				3	3	6
missense			43	1	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	4	4

Variants in CD180

This is a list of pathogenic ClinVar variants found in the CD180 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-67182954-A-G		not specified	Uncertain significance (Jan 16, 2024)
5-67183008-G-A		not specified	Uncertain significance (Jun 12, 2023)
5-67183037-C-T			Likely benign (Apr 04, 2018)
5-67183041-C-G		not specified	Uncertain significance (Sep 13, 2023)
5-67183060-T-C		not specified	Uncertain significance (Jan 03, 2024)
5-67183091-C-T			Benign (Jun 04, 2018)
5-67183180-T-G		not specified	Uncertain significance (Jan 23, 2024)
5-67183240-C-T		not specified	Likely benign (Jul 05, 2023)
5-67183269-A-G		not specified	Uncertain significance (Oct 28, 2023)
5-67183393-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-67183398-T-G		not specified	Uncertain significance (Oct 20, 2023)
5-67183429-G-A		not specified	Uncertain significance (Feb 17, 2023)
5-67183454-A-T		not specified	Uncertain significance (Jun 23, 2023)
5-67183555-T-C			Benign (Jun 12, 2018)
5-67183573-G-C		not specified	Uncertain significance (Dec 09, 2023)
5-67183584-G-A		not specified	Uncertain significance (Aug 14, 2023)
5-67183600-C-A		not specified	Uncertain significance (Mar 29, 2022)
5-67183649-C-T			Benign (May 29, 2018)
5-67183744-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-67183753-C-T		not specified	Uncertain significance (Nov 17, 2022)
5-67183800-G-A		not specified	Uncertain significance (Jan 05, 2022)
5-67183869-T-G		not specified	Uncertain significance (Oct 30, 2023)
5-67183920-G-A		not specified	Uncertain significance (Jun 13, 2023)
5-67183927-T-G		not specified	Uncertain significance (Sep 13, 2023)
5-67184014-C-T		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD180	protein_coding	protein_coding	ENST00000256447	3	14525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000684	0.916	125341	2	404	125747	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	333	343	0.971	0.0000171	4416
Missense in Polyphen		87	92.806	0.93744		1329
Synonymous	-0.303	143	138	1.03	0.00000740	1279
Loss of Function	1.59	9	15.8	0.569	6.70e-7	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00187
Ashkenazi Jewish	0.00647	0.00647
East Asian	0.000222	0.000217
Finnish	0.00130	0.00129
European (Non-Finnish)	0.00157	0.00156
Middle Eastern	0.000222	0.000217
South Asian	0.00229	0.00219
Other	0.000981	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May cooperate with MD-1 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) in B-cells. Leads to NF-kappa-B activation. Also involved in the life/death decision of B-cells (By similarity). {ECO:0000250}.
• Pathway: Regulation of toll-like receptor signaling pathway;Toll-Like Receptors Cascades;Innate Immune System;Immune System;Toll Like Receptor 4 (TLR4) Cascade (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• pHI: 0.0612
• hipred: N
• hipred_score: 0.112
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.769

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd180
• Phenotype: hematopoietic 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); renal/urinary system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: B cell proliferation involved in immune response;inflammatory response;positive regulation of lipopolysaccharide-mediated signaling pathway;innate immune response;cellular response to lipopolysaccharide
• Cellular component: extracellular space;plasma membrane;integral component of membrane;extracellular matrix
• Molecular function: protein binding