LY6H

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

Basic information

Region (hg38): 8:143157914-143160711

Links

ENSG00000176956 ∙ NCBI:4062 ∙ OMIM:603625 ∙ HGNC:6728 ∙ Uniprot:O94772 ∙ 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 LY6H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6H 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			7	1		8
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in LY6H

This is a list of pathogenic ClinVar variants found in the LY6H region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143158296-C-T		not specified	Uncertain significance (Jan 04, 2022)
8-143158335-G-A		not specified	Likely benign (Sep 16, 2021)
8-143158362-C-T		not specified	Uncertain significance (May 23, 2023)
8-143158381-A-C		not specified	Uncertain significance (Dec 16, 2023)
8-143158922-G-A		not specified	Uncertain significance (Jun 16, 2023)
8-143159590-G-A		not specified	Uncertain significance (Jun 05, 2023)
8-143159648-T-C		not specified	Uncertain significance (Oct 05, 2021)
8-143159662-C-G		not specified	Uncertain significance (Sep 26, 2022)
8-143159668-G-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6H	protein_coding	protein_coding	ENST00000414417	4	2798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.168	0.777	125721	0	2	125723	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.606	67	82.5	0.812	0.00000446	1033
Missense in Polyphen		17	27.831	0.61083		302
Synonymous	-0.179	41	39.6	1.04	0.00000260	338
Loss of Function	1.58	2	6.28	0.319	4.36e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro inhibits alpha-3:beta-4-containing nAChRs maximum response. May play a role in the intracellular trafficking of alpha-7-containing nAChRs and may inhibit their expression at the cell surface. Seems to inhibit alpha-7/CHRNA7 signaling in hippocampal neurons. {ECO:0000250|UniProtKB:F1LNW6, ECO:0000250|UniProtKB:Q9WUC3}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• loftool: 0.423
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.322
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6h

Gene ontology

• Biological process: nervous system development;animal organ morphogenesis;acetylcholine receptor signaling pathway;negative regulation of signaling receptor activity
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: protein binding;acetylcholine receptor inhibitor activity;acetylcholine receptor binding