LILRA6

protein-coding

leukocyte immunoglobulin like receptor A6, the group of CD molecules|Activating leukocyte immunoglobulin like receptors

Gene summary

Predicted to enable inhibitory MHC class I receptor activity. Predicted to be involved in cytokine-mediated signaling pathway and immune response-inhibiting cell surface receptor signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LILRB6

MANE transcript

NM_024318.5

Inheritance

—

ClinVar variants

U:10B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr19:54,236,590-54,242,790

External References & Databases

Ensembl (ENSG00000244482)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 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 LILRA6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 9

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024318.5. 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				6 clinvar		6
missense			7 clinvar	1 clinvar		8
nonsense			2 clinvar			2
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	8	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024318.5	RefSeq	NP_077294.3	8	MANE Select
ENST00000396365.7	Ensembl	ENSP00000379651.2	8	MANE Select
ENST00000245621.6	Ensembl	ENSP00000245621.4	7	Standard
ENST00000430421.5	Ensembl	ENSP00000412929.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Osteoclast differentiation - Homo sapiens (human)
Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

adaptive immune response

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396365
Coding exons: 8
Length: 25913
Individuals with no LoFs: 125703
Homozygous LoFs: 6
Heterozygous LoFs: 30
Defined: 125739
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.429	257	238	1.08	0.0000128	2844
Missense (PolyPhen)		69	72.776	0.94811		973
Synonymous	-2.02	129	103	1.25	0.00000605	917
Loss of Function	1.85	10	18.6	0.537	8.91e-7	227

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00025	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00025	0.00021	rare
South Asian	0.00017	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as receptor for class I MHC antigens. {ECO:0000250}.;

Recessive Scores

pRec: 0.0660

Intolerance Scores

LoFtool: 0.778
RVIS EVS: 1.89
RVIS percentile EVS: 97.3

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0762

Gene Damage Prediction

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