LY75

lymphocyte antigen 75, the group of CD molecules|Scavenger receptors|Minor histocompatibility antigens|C-type lectin domain containing

Basic information

Region (hg38): 2:159803355-159904756

Links

ENSG00000054219 ∙ NCBI:4065 ∙ OMIM:604524 ∙ HGNC:6729 ∙ Uniprot:O60449 ∙ 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 LY75 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY75 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	2	5
missense			11	4	5	20
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	11	7	7

Variants in LY75

This is a list of pathogenic ClinVar variants found in the LY75 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-159805071-C-G		not specified	Uncertain significance (Sep 12, 2023)
2-159805093-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-159805099-C-G			Likely benign (Aug 01, 2023)
2-159805160-C-T		not specified	Uncertain significance (Aug 20, 2024)
2-159805161-G-A			Likely benign (Mar 28, 2018)
2-159835606-G-A			Likely benign (Dec 31, 2019)
2-159850034-C-T			Likely benign (Apr 01, 2023)
2-159850420-G-T			Likely benign (Aug 01, 2023)
2-159852215-G-A		not specified	Uncertain significance (Aug 28, 2023)
2-159854943-T-C			Benign (Nov 20, 2018)
2-159872571-A-G			Benign (Nov 20, 2018)
2-159875493-G-A		not specified	Uncertain significance (Oct 01, 2024)
2-159875633-G-A			Benign (Dec 26, 2018)
2-159878363-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-159878679-C-A			Benign (Dec 26, 2018)
2-159878680-C-A			Benign (Dec 26, 2018)
2-159879264-C-T			Benign (Dec 26, 2018)
2-159879291-C-T			Likely benign (Dec 26, 2018)
2-159881206-G-A			Benign (Dec 26, 2018)
2-159882292-G-A			Benign (Nov 20, 2018)
2-159893932-C-T		not specified	Uncertain significance (Jun 11, 2024)
2-159898829-T-G		not specified	Uncertain significance (Jul 15, 2021)
2-159898840-A-G		not specified	Uncertain significance (Jan 17, 2023)
2-159898879-A-C		not specified	Uncertain significance (Apr 26, 2023)
2-159899016-G-A			Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY75	protein_coding	protein_coding	ENST00000554112	39	132899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.45e-46	0.00420	125175	1	572	125748	0.00228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0170	963	962	1.00	0.0000483	12432
Missense in Polyphen		502	518.78	0.96765		7005
Synonymous	0.980	313	336	0.932	0.0000176	3239
Loss of Function	2.20	84	109	0.773	0.00000509	1342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00730	0.00725
Ashkenazi Jewish	0.00974	0.00967
East Asian	0.00174	0.00174
Finnish	0.00162	0.00162
European (Non-Finnish)	0.00158	0.00152
Middle Eastern	0.00174	0.00174
South Asian	0.00245	0.00232
Other	0.00351	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen- processing compartment (By similarity). Causes reduced proliferation of B-lymphocytes. {ECO:0000250}.

Recessive Scores

• pRec: 0.371

Intolerance Scores

• loftool: 0.998
• rvis_EVS: 3.82
• rvis_percentile_EVS: 99.63

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: N
• hipred_score: 0.240
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ly75
• Phenotype: immune system 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: ly75
• Affected structure: atrium
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: endocytosis;inflammatory response;immune response
• Cellular component: integral component of plasma membrane;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;carbohydrate binding;signaling receptor activity