LY6D

protein-coding

lymphocyte antigen 6 family member D, the group of LY6/PLAUR domain containing

Gene summary

Predicted to be involved in lymphocyte differentiation. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_003695.3

Inheritance

—

ClinVar variants

U:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr8:142,784,882-142,786,539

External References & Databases

Ensembl (ENSG00000167656)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 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 LY6D variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003695.3. 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						0
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003695.3	RefSeq	NP_003686.1	3	MANE Select
ENST00000301263.5	Ensembl	ENSP00000301263.4	3	MANE Select
ENST00001100173.1	Ensembl	ENSP00000769979.1	3	Standard
ENST00001100174.1	Ensembl	ENSP00000769980.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

cell adhesion
lymphocyte differentiation
response to stilbenoid

Cellular Component

extracellular region
plasma membrane
cell surface
membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301263
Coding exons: 3
Length: 1713
Individuals with no LoFs: 125183
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125207
p: 0.0000958

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.610	62	77.1	0.804	0.00000456	810
Missense (PolyPhen)		13	16.853	0.77139		175
Synonymous	0.0738	36	36.6	0.984	0.00000235	278
Loss of Function	0.0424	2	2.07	0.968	8.75e-8	25

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a specification marker at earliest stage specification of lymphocytes between B- and T-cell development. Marks the earliest stage of B-cell specification.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.761
RVIS EVS: 0.3
RVIS percentile EVS: 72.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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