LY6G6C

lymphocyte antigen 6 family member G6C, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 6:31718648-31721746

Previous symbols: [ "C6orf24" ]

Links

ENSG00000204421 ∙ NCBI:80740 ∙ OMIM:610435 ∙ HGNC:13936 ∙ Uniprot:O95867 ∙ 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 LY6G6C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G6C 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	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	8	1	1

Variants in LY6G6C

This is a list of pathogenic ClinVar variants found in the LY6G6C region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31719160-G-T		not specified	Uncertain significance (Jan 03, 2024)
6-31719167-G-A		not specified	Uncertain significance (Aug 17, 2022)
6-31719176-C-T		not specified	Uncertain significance (Aug 02, 2023)
6-31719235-T-C		not specified	Likely benign (Feb 15, 2023)
6-31719250-G-C			Benign (May 03, 2018)
6-31719284-G-A		not specified	Uncertain significance (Jan 24, 2024)
6-31719300-C-G		not specified	Uncertain significance (May 11, 2022)
6-31720149-C-T		not specified	Uncertain significance (Jan 31, 2023)
6-31720150-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-31720152-T-G		not specified	Uncertain significance (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G6C	protein_coding	protein_coding	ENST00000375819	3	3198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000493	0.458	125712	0	34	125746	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.429	63	73.3	0.859	0.00000415	792
Missense in Polyphen		24	29.608	0.81058		310
Synonymous	1.07	21	28.2	0.744	0.00000131	266
Loss of Function	0.130	5	5.32	0.939	2.26e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000243	0.000237
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0976

Intolerance Scores

• loftool: 0.575
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.45

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.213
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6g6c

Gene ontology

• Biological process: response to bacterium;protein homooligomerization
• Cellular component: extracellular region;plasma membrane;external side of plasma membrane;anchored component of membrane;protein-containing complex
• Molecular function: identical protein binding