LY6G6D

lymphocyte antigen 6 family member G6D, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 6:31715347-31717919

Previous symbols: [ "C6orf23" ]

Links

ENSG00000244355 ∙ NCBI:58530 ∙ OMIM:606038 ∙ HGNC:13935 ∙ Uniprot:O95868 ∙ 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 LY6G6D gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G6D 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			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in LY6G6D

This is a list of pathogenic ClinVar variants found in the LY6G6D region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31715520-A-G		not specified	Uncertain significance (Jan 10, 2023)
6-31715561-G-A		not specified	Uncertain significance (Sep 30, 2021)
6-31715579-G-A		not specified	Uncertain significance (Apr 17, 2023)
6-31715583-G-A		not specified	Likely benign (Sep 16, 2021)
6-31717619-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-31717778-C-A		not specified	Uncertain significance (Dec 18, 2023)
6-31717799-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G6D	protein_coding	protein_coding	ENST00000375825	3	2449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0326	0.830	125731	0	14	125745	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.104	77	79.6	0.967	0.00000445	846
Missense in Polyphen		5	5.0748	0.98526		50
Synonymous	1.06	26	33.9	0.768	0.00000206	285
Loss of Function	1.17	3	6.12	0.490	4.45e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000731	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0865

Intolerance Scores

• loftool: 0.552
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.158
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Ly6g6d

Gene ontology

• Biological process: protein homooligomerization;acetylcholine receptor signaling pathway;negative regulation of signaling receptor activity
• Cellular component: extracellular region;plasma membrane;external side of plasma membrane;filopodium;anchored component of membrane;protein-containing complex
• Molecular function: acetylcholine receptor inhibitor activity;identical protein binding