LILRA6

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

Basic information

Region (hg38): 19:54236591-54242791

Previous symbols: [ "LILRB6" ]

Links

ENSG00000244482 ∙ NCBI:79168 ∙ ∙ HGNC:15495 ∙ Uniprot:Q6PI73 ∙ 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 LILRA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA6 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				2		2
missense			8	1	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	10	4	1

Variants in LILRA6

This is a list of pathogenic ClinVar variants found in the LILRA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54239031-C-G		not specified	Uncertain significance (Oct 06, 2021)
19-54239920-T-A			Likely benign (Apr 01, 2022)
19-54240399-T-C		not specified	Uncertain significance (Sep 17, 2021)
19-54240482-C-C			Likely benign (Apr 01, 2023)
19-54240484-G-G		not specified	Uncertain significance (Sep 15, 2021)
19-54240487-A-A		not specified	Uncertain significance (Sep 15, 2021)
19-54240559-C-T		not specified	Uncertain significance (Sep 30, 2021)
19-54240882-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-54240924-G-C		not specified	Uncertain significance (Jun 23, 2021)
19-54240925-G-C		not specified	Likely benign (Jun 23, 2021)
19-54240939-G-C		not specified	Uncertain significance (Aug 17, 2021)
19-54241016-T-C		not specified	Uncertain significance (Jul 13, 2021)
19-54241032-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-54241060-G-A			Likely benign (Jan 01, 2024)
19-54241620-C-T		not specified	Benign (Mar 29, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRA6	protein_coding	protein_coding	ENST00000396365	8	25913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000390	0.958	125703	6	30	125739	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.429	257	238	1.08	0.0000128	2844
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000250	0.000250
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000211
Middle Eastern	0.00	0.00
South Asian	0.000167	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as receptor for class I MHC antigens. {ECO:0000250}.
• Pathway: Osteoclast differentiation - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0660

Intolerance Scores

• loftool: 0.778
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.3

Haploinsufficiency Scores

• pHI: 0.0405
• hipred: N
• hipred_score: 0.187
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0762

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response
• Cellular component: integral component of membrane