LY6G5B

lymphocyte antigen 6 family member G5B, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 6:31669976-31673776

Previous symbols: [ "C6orf19" ]

Links

ENSG00000240053 ∙ NCBI:58496 ∙ OMIM:610433 ∙ HGNC:13931 ∙ Uniprot:Q8NDX9 ∙ 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 LY6G5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G5B 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	0	0	12	1	2

Variants in LY6G5B

This is a list of pathogenic ClinVar variants found in the LY6G5B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31670030-C-T			Benign (May 11, 2021)
6-31670957-G-A		not specified	Uncertain significance (Jun 03, 2022)
6-31671193-C-T			Benign (Oct 18, 2018)
6-31671207-C-G		not specified	Uncertain significance (Oct 12, 2022)
6-31671261-G-A		not specified	Uncertain significance (Apr 01, 2024)
6-31671273-C-T		not specified	Uncertain significance (Apr 12, 2024)
6-31671867-T-C		not specified	Uncertain significance (May 11, 2022)
6-31671876-G-A		not specified	Uncertain significance (May 01, 2022)
6-31671884-G-A		not specified	Likely benign (Nov 10, 2022)
6-31671887-C-G		not specified	Uncertain significance (Jan 04, 2022)
6-31671893-T-C		not specified	Uncertain significance (May 15, 2024)
6-31671914-C-T		not specified	Uncertain significance (Oct 12, 2022)
6-31672030-G-C		not specified	Uncertain significance (Oct 26, 2022)
6-31672085-T-C		not specified	Uncertain significance (Jan 22, 2024)
6-31672121-T-G		not specified	Uncertain significance (Jan 17, 2024)
6-31672131-G-C		not specified	Uncertain significance (Dec 01, 2022)
6-31672137-A-G		not specified	Uncertain significance (Nov 08, 2021)
6-31672224-A-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G5B	protein_coding	protein_coding	ENST00000375864	3	3610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000818	0.321	125517	0	22	125539	0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0972	120	117	1.03	0.00000655	1286
Missense in Polyphen		44	35.791	1.2294		442
Synonymous	0.885	39	46.7	0.835	0.00000254	414
Loss of Function	0.172	8	8.54	0.936	4.31e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000986	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.201

Intolerance Scores

• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6g5b

Gene ontology

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