LY6D

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

Basic information

Region (hg38): 8:142784881-142786539

Links

ENSG00000167656 ∙ NCBI:8581 ∙ OMIM:606204 ∙ HGNC:13348 ∙ Uniprot:Q14210 ∙ 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 LY6D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6D 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in LY6D

This is a list of pathogenic ClinVar variants found in the LY6D region.

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

Position	Type	Phenotype	Significance	ClinVar
8-142785244-C-T		not specified	Uncertain significance (Aug 04, 2023)
8-142785300-C-T		not specified	Uncertain significance (Feb 22, 2023)
8-142785307-G-T		not specified	Uncertain significance (Jan 08, 2024)
8-142785411-G-A		not specified	Uncertain significance (Apr 24, 2024)
8-142785676-G-T		not specified	Uncertain significance (May 05, 2023)
8-142786473-G-A		not specified	Uncertain significance (Nov 01, 2022)
8-142786502-C-A		not specified	Uncertain significance (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6D	protein_coding	protein_coding	ENST00000301263	3	1713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0260	0.581	125183	0	24	125207	0.0000958

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.610	62	77.1	0.804	0.00000456	810
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000151
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.761
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: N
• hipred_score: 0.123
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6d

Gene ontology

• Biological process: cell adhesion;lymphocyte differentiation;response to stilbenoid
• Cellular component: extracellular region;plasma membrane;cell surface;membrane;anchored component of membrane