LY6G6F

lymphocyte antigen 6 family member G6F, the group of V-set domain containing|LY6/PLAUR domain containing

Basic information

Region (hg38): 6:31706865-31710679

Previous symbols: [ "LY6G6D", "C6orf21" ]

Links

ENSG00000204424 ∙ NCBI:259215 ∙ OMIM:611404 ∙ HGNC:13933 ∙ Uniprot:Q5SQ64 ∙ 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 LY6G6F gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G6F 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			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in LY6G6F

This is a list of pathogenic ClinVar variants found in the LY6G6F region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31707506-C-A			Benign (Feb 20, 2018)
6-31707517-C-T		not specified	Uncertain significance (Jan 19, 2022)
6-31707523-A-G		not specified	Uncertain significance (Mar 12, 2024)
6-31707538-G-A		not specified	Uncertain significance (Jul 05, 2023)
6-31707631-A-C		not specified	Uncertain significance (Feb 07, 2023)
6-31707680-G-C		not specified	Uncertain significance (Apr 25, 2023)
6-31707718-T-G		not specified	Uncertain significance (Jan 10, 2023)
6-31707886-C-T		not specified	Uncertain significance (May 17, 2023)
6-31707904-C-A		not specified	Uncertain significance (Sep 14, 2023)
6-31707985-T-G		not specified	Uncertain significance (Feb 15, 2023)
6-31707993-C-T		not specified	Uncertain significance (Nov 23, 2021)
6-31708003-C-T		not specified	Uncertain significance (Oct 13, 2021)
6-31710088-C-G		not specified	Uncertain significance (Mar 04, 2024)
6-31710166-G-T		not specified	Uncertain significance (Oct 05, 2023)
6-31710358-C-T		not specified	Uncertain significance (Dec 11, 2023)
6-31710397-A-G		not specified	Uncertain significance (Apr 17, 2023)
6-31710399-A-T		not specified	Uncertain significance (Mar 03, 2022)
6-31710411-C-T		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G6F	protein_coding	protein_coding	ENST00000375832	6	10942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.56e-7	0.548	125643	0	104	125747	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.677	147	172	0.855	0.00000935	1896
Missense in Polyphen		29	34.104	0.85035		356
Synonymous	1.08	59	70.5	0.837	0.00000400	630
Loss of Function	0.873	11	14.6	0.753	7.10e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000834	0.000828
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000470	0.000466
Middle Eastern	0.00	0.00
South Asian	0.000654	0.000653
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the downstream signal transduction pathways involving GRB2 and GRB7. {ECO:0000269|PubMed:12852788}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.0865

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.276
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6g6f

Gene ontology

• Biological process: platelet degranulation
• Cellular component: plasma membrane;integral component of membrane;platelet alpha granule membrane