LY6G5C

lymphocyte antigen 6 family member G5C, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 6:31676684-31684040

Previous symbols: [ "C6orf20" ]

Links

ENSG00000204428 ∙ NCBI:80741 ∙ OMIM:610434 ∙ HGNC:13932 ∙ Uniprot:Q5SRR4 ∙ 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 LY6G5C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G5C 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	5	0	0

Variants in LY6G5C

This is a list of pathogenic ClinVar variants found in the LY6G5C region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31676976-C-G		not specified	Uncertain significance (Mar 25, 2024)
6-31677042-G-A		not specified	Uncertain significance (Jul 27, 2023)
6-31677071-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-31677101-C-T		not specified	Uncertain significance (Jul 06, 2021)
6-31679267-A-G			Likely benign (Apr 01, 2022)
6-31680274-C-G		not specified	Uncertain significance (Jan 08, 2024)
6-31680303-G-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G5C	protein_coding	protein_coding	ENST00000383237	3	7357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.405	0.560	123443	0	2	123445	0.00000810

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	49	83.4	0.588	0.00000423	986
Missense in Polyphen		11	22.369	0.49176		281
Synonymous	0.373	29	31.7	0.916	0.00000173	285
Loss of Function	1.68	1	5.10	0.196	3.03e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000658
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in hematopoietic cell differentiation.

Intolerance Scores

• loftool: 0.469
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.243
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0226

Mouse Genome Informatics

• Gene name: Ly6g5c

Gene ontology

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