LY6K

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

Basic information

Region (hg38): 8:142700111-142705127

Links

ENSG00000160886 ∙ NCBI:54742 ∙ OMIM:615093 ∙ HGNC:24225 ∙ Uniprot:Q17RY6 ∙ 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 LY6K gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6K 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in LY6K

This is a list of pathogenic ClinVar variants found in the LY6K region.

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

Position	Type	Phenotype	Significance	ClinVar
8-142700531-G-T		not specified	Uncertain significance (Aug 11, 2024)
8-142700532-C-T		not specified	Uncertain significance (Apr 06, 2024)
8-142700540-G-C		not specified	Uncertain significance (Apr 05, 2023)
8-142700573-T-A		not specified	Uncertain significance (Apr 24, 2024)
8-142700577-C-A		not specified	Uncertain significance (May 05, 2023)
8-142700582-G-T		not specified	Uncertain significance (Nov 13, 2024)
8-142700588-C-G		not specified	Uncertain significance (Nov 30, 2022)
8-142701606-G-C		not specified	Uncertain significance (Jun 11, 2021)
8-142701610-C-A		not specified	Uncertain significance (Sep 13, 2023)
8-142701648-C-T		not specified	Uncertain significance (Jan 29, 2024)
8-142701670-G-C		not specified	Uncertain significance (Aug 14, 2024)
8-142701711-T-A		not specified	Uncertain significance (Nov 10, 2022)
8-142703093-A-G		not specified	Uncertain significance (Oct 03, 2024)
8-142703102-C-T		not specified	Uncertain significance (Oct 13, 2021)
8-142703130-C-G		not specified	Uncertain significance (Feb 28, 2023)
8-142703132-G-A		not specified	Uncertain significance (Sep 30, 2024)
8-142703168-G-A		not specified	Uncertain significance (Dec 01, 2022)
8-142703174-C-T		not specified	Uncertain significance (Jun 22, 2021)
8-142703181-T-C		not specified	Uncertain significance (Apr 28, 2022)
8-142703201-T-C		not specified	Uncertain significance (Apr 28, 2022)
8-142703219-T-C		not specified	Uncertain significance (Apr 01, 2024)
8-142703229-G-A		not specified	Uncertain significance (Jan 04, 2024)
8-142703253-C-G		not specified	Uncertain significance (Apr 18, 2023)
8-142703354-G-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6K	protein_coding	protein_coding	ENST00000292430	3	5017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0142	0.694	125703	0	16	125719	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	84	97.4	0.862	0.00000593	1055
Missense in Polyphen		17	17.744	0.95806		233
Synonymous	0.667	34	39.3	0.865	0.00000251	323
Loss of Function	0.611	3	4.38	0.685	2.65e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for sperm migration into the oviduct and male fertility by controlling binding of sperm to zona pellucida (By similarity). May play a role in cell growth (PubMed:18089789). {ECO:0000250|UniProtKB:Q9CWP4, ECO:0000269|PubMed:18089789}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Haploinsufficiency Scores

• pHI: 0.0856
• hipred: N
• hipred_score: 0.146
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6k
• Phenotype: reproductive system phenotype

Gene ontology

• Cellular component: acrosomal vesicle;extracellular region;plasma membrane;anchored component of membrane;membrane raft