LY9

lymphocyte antigen 9, the group of Immunoglobulin like domain containing|CD molecules

Basic information

Region (hg38): 1:160796073-160828261

Links

ENSG00000122224 ∙ NCBI:4063 ∙ OMIM:600684 ∙ HGNC:6730 ∙ Uniprot:Q9HBG7 ∙ 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 LY9 gene.

• Inborn genetic diseases (33 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY9 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				1		1
missense			31	2	2	35
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	2

Variants in LY9

This is a list of pathogenic ClinVar variants found in the LY9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160796226-T-C			Likely benign (Dec 15, 2017)
1-160796285-A-C		not specified	Uncertain significance (Oct 12, 2022)
1-160796301-C-G		not specified	Uncertain significance (Feb 14, 2023)
1-160799779-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-160799801-T-C		not specified	Uncertain significance (Jul 21, 2022)
1-160799805-AG-A			association (Aug 30, 2022)
1-160799846-C-T		not specified	Uncertain significance (Oct 05, 2022)
1-160799897-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-160799899-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-160799900-G-A		LY9-related disorder	Likely benign (Jan 10, 2024)
1-160799910-A-C		not specified	Uncertain significance (Nov 04, 2023)
1-160799918-C-A		not specified	Uncertain significance (Nov 09, 2023)
1-160799978-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-160813645-A-G		not specified	Uncertain significance (Feb 07, 2023)
1-160813712-G-A		not specified	Uncertain significance (Mar 16, 2022)
1-160813716-T-G		not specified	Uncertain significance (Jul 25, 2023)
1-160813725-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-160813738-G-C		not specified	Uncertain significance (Oct 31, 2022)
1-160813767-C-A			Benign (Dec 15, 2017)
1-160813888-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-160814461-G-T		not specified	Uncertain significance (Feb 10, 2022)
1-160814513-G-A		not specified	Likely benign (Jul 09, 2021)
1-160814530-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-160814566-A-G		not specified	Uncertain significance (Oct 02, 2023)
1-160814608-G-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY9	protein_coding	protein_coding	ENST00000263285	10	32188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.60e-13	0.240	125723	0	12	125735	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.217	368	356	1.03	0.0000183	4256
Missense in Polyphen		83	90.545	0.91667		1201
Synonymous	0.800	134	146	0.916	0.00000828	1331
Loss of Function	1.08	23	29.3	0.785	0.00000162	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000250	0.000244
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000372	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity). {ECO:0000250|UniProtKB:Q01965, ECO:0000269|PubMed:22184727, ECO:0000269|PubMed:22989874}.
• Pathway: TCR (Consensus)

Intolerance Scores

• loftool: 0.966
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

• pHI: 0.0472
• hipred: N
• hipred_score: 0.112
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly9
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;positive regulation of interleukin-17 production;innate immune response;T-helper 17 cell lineage commitment
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: molecular_function