LY75

protein-coding

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

Gene summary

Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in receptor-mediated endocytosis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002349.4

Inheritance

—

ClinVar variants

U:21B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr2:159,803,355-159,904,756

External References & Databases

Ensembl (ENSG00000054219)

Transcript & Mutation Effects

hg38 • Region Span ~101.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LY75 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 18

not providedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002349.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	2 clinvar	6
missense			18 clinvar	5 clinvar	5 clinvar	28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	21	8	7	36

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002349.4	RefSeq	NP_002340.2	35	MANE Select
ENST00000263636.5	Ensembl	ENSP00000263636.4	35	MANE Select
ENST00000971950.1	Ensembl	ENSP00000642009.1	34	Standard
ENST00000971950.2	Ensembl	ENSP00000642009.1	34	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ly75	Danio rerio	Structure: atrium Quality: dilated abnormal

Gene / Model

Organism

Observed Phenotype

ly75

Danio rerio

Structure: atrium

Quality: dilated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endocytosis
inflammatory response
immune response

Molecular Function

transmembrane signaling receptor activity
carbohydrate binding
signaling receptor activity

Cellular Component

integral component of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000554112
Coding exons: 39
Length: 132899
Individuals with no LoFs: 125175
Homozygous LoFs: 1
Heterozygous LoFs: 572
Defined: 125748
p: 0.00228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0170	963	962	1.00	0.0000483	12432
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0055	0.0054	notable
Latino/Admixed American	0.0018	0.0016	notable
Ashkenazi Jewish	0.0097	0.0097	notable
East Asian	0.0017	0.0017	notable
Finnish	0.0016	0.0016	notable
European (Non-Finnish)	0.0016	0.0015	notable
South Asian	0.0024	0.0023	notable
Other	0.0035	0.0034	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.212

Gene Damage Prediction

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